Variant report

Variant	rs12138526
Chromosome Location	chr1:247268302-247268303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr1:247267149-247268523	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA1	chr1:247266765-247268596	K562	blood:	n/a	n/a
3	JUN	chr1:247266856-247268739	K562	blood:	n/a	chr1:247267812-247267825
4	SIN3A	chr1:247268217-247268823	H1-hESC	embryonic stem cell:	n/a	n/a
5	CBX3	chr1:247267380-247268517	K562	blood:	n/a	n/a
6	MXI1	chr1:247266784-247268494	SK-N-SH	brain:	n/a	n/a
7	HCFC1	chr1:247266954-247268302	Hela-S3	cervix:	n/a	n/a
8	MYC	chr1:247268255-247268383	NB4	blood:	n/a	n/a
9	POLR2A	chr1:247268296-247268482	H1-hESC	embryonic stem cell:	n/a	n/a
10	GATA2	chr1:247266982-247268615	SH-SY5Y	brain:	n/a	n/a
11	CBX3	chr1:247266326-247268517	K562	blood:	n/a	n/a
12	MAX	chr1:247268131-247268547	H1-hESC	embryonic stem cell:	n/a	n/a
13	BHLHE40	chr1:247267089-247268349	HepG2	liver:	n/a	chr1:247267799-247267812
14	MAX	chr1:247268064-247268488	H1-hESC	embryonic stem cell:	n/a	n/a
15	RCOR1	chr1:247268227-247268418	K562	blood:	n/a	n/a
16	MXI1	chr1:247268292-247268675	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:247266956-247268636	H1-hESC	embryonic stem cell:	n/a	n/a
18	NR2F2	chr1:247266885-247268582	K562	blood:	n/a	n/a
19	POLR2A	chr1:247267018-247268392	HepG2	liver:	n/a	n/a
20	MAX	chr1:247268151-247268778	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr1:247267019-247268405	NB4	blood:	n/a	chr1:247267801-247267810
22	BHLHE40	chr1:247267007-247268654	K562	blood:	n/a	chr1:247267799-247267812
23	MAX	chr1:247268104-247268452	K562	blood:	n/a	n/a
24	MAX	chr1:247268240-247268390	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247266988..247268956-chr1:247494459..247496057,2	MCF-7	breast:
2	chr1:247240434..247242888-chr1:247264757..247270232,6	K562	blood:
3	chr1:247262370..247270931-chr1:247272613..247278774,19	MCF-7	breast:
4	chr1:247240729..247243451-chr1:247267537..247269103,3	MCF-7	breast:
5	chr1:247249215..247251294-chr1:247266275..247268905,2	MCF-7	breast:
6	chr1:247092719..247096472-chr1:247266171..247268660,3	MCF-7	breast:
7	chr1:247239357..247243782-chr1:247265039..247269405,6	MCF-7	breast:
8	chr1:247169768..247172852-chr1:247266315..247269719,3	K562	blood:
9	chr1:247236513..247243563-chr1:247264600..247268970,10	K562	blood:
10	chr1:247140883..247143696-chr1:247267943..247270450,3	MCF-7	breast:
11	chr1:247093046..247095250-chr1:247265472..247268873,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF669	TF binding region
ENSG00000153207	Chromatin interaction
ENSG00000221953	Chromatin interaction
ENSG00000135747	Chromatin interaction
ENSG00000228982	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000197472	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1007457	0.81[ASN][1000 genomes]
rs10754536	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802463	0.81[ASN][1000 genomes]
rs10802466	0.87[ASN][1000 genomes]
rs10802468	0.98[ASN][1000 genomes]
rs10802469	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10924907	0.87[ASN][1000 genomes]
rs10924909	0.91[ASN][1000 genomes]
rs10924910	0.92[ASN][1000 genomes]
rs10924912	0.97[ASN][1000 genomes]
rs10924914	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10924915	0.97[ASN][1000 genomes]
rs10924917	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924919	0.97[ASN][1000 genomes]
rs10924924	0.81[ASN][1000 genomes]
rs11801681	0.82[ASN][1000 genomes]
rs12080836	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12084753	0.91[ASN][1000 genomes]
rs12094740	0.91[ASN][1000 genomes]
rs12119918	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120049	0.81[ASN][1000 genomes]
rs12121363	0.82[ASN][1000 genomes]
rs12128943	0.82[ASN][1000 genomes]
rs12129591	0.81[ASN][1000 genomes]
rs12131094	0.82[ASN][1000 genomes]
rs12138686	0.95[ASN][1000 genomes]
rs12141797	0.91[ASN][1000 genomes]
rs12144733	0.91[ASN][1000 genomes]
rs12144854	0.82[ASN][1000 genomes]
rs12691533	0.92[ASN][1000 genomes]
rs12723583	0.81[ASN][1000 genomes]
rs13376442	0.91[ASN][1000 genomes]
rs1552988	0.91[ASN][1000 genomes]
rs2055190	0.90[ASN][1000 genomes]
rs2270616	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2379192	0.88[ASN][1000 genomes]
rs2379193	0.91[ASN][1000 genomes]
rs2890101	0.92[ASN][1000 genomes]
rs2890102	0.91[ASN][1000 genomes]
rs2890103	0.91[ASN][1000 genomes]
rs2890104	0.91[ASN][1000 genomes]
rs2890105	0.91[ASN][1000 genomes]
rs2890106	0.91[ASN][1000 genomes]
rs34273666	0.91[ASN][1000 genomes]
rs34350972	0.91[ASN][1000 genomes]
rs35314391	0.91[ASN][1000 genomes]
rs35452630	0.91[ASN][1000 genomes]
rs35511369	0.91[ASN][1000 genomes]
rs3736325	0.98[ASN][1000 genomes]
rs3806269	0.88[ASN][1000 genomes]
rs3892246	0.91[ASN][1000 genomes]
rs3892516	0.91[ASN][1000 genomes]
rs41305955	0.88[ASN][1000 genomes]
rs4925692	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4925701	0.81[ASN][1000 genomes]
rs4925702	0.82[ASN][1000 genomes]
rs4925703	0.81[ASN][1000 genomes]
rs4925704	0.82[ASN][1000 genomes]
rs55649449	0.88[ASN][1000 genomes]
rs57003817	0.91[ASN][1000 genomes]
rs60293371	0.91[ASN][1000 genomes]
rs60677310	0.91[ASN][1000 genomes]
rs60794525	0.91[ASN][1000 genomes]
rs6426217	0.85[ASN][1000 genomes]
rs6426218	0.92[ASN][1000 genomes]
rs6426220	0.87[ASN][1000 genomes]
rs6658298	0.90[ASN][1000 genomes]
rs6659256	0.91[ASN][1000 genomes]
rs6664157	0.87[ASN][1000 genomes]
rs6669242	0.92[ASN][1000 genomes]
rs6680033	0.82[ASN][1000 genomes]
rs6681227	0.92[ASN][1000 genomes]
rs6693464	0.90[ASN][1000 genomes]
rs6695894	0.81[ASN][1000 genomes]
rs6699898	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702419	0.92[ASN][1000 genomes]
rs7412787	0.90[ASN][1000 genomes]
rs7549674	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
10	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
14	nsv999352	chr1:247180668-247307074	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv535421	chr1:247180668-247307074	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv997687	chr1:247180668-247348847	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv535422	chr1:247180668-247348847	ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
20	nsv1014012	chr1:247207932-247289138	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv873428	chr1:247226986-247346189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
22	nsv873429	chr1:247230809-247288469	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv549547	chr1:247233156-247281769	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv873430	chr1:247233156-247291400	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv873431	chr1:247242836-247297502	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12138526	ZNF669	cis	Nerve Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247265600-247268600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:247265800-247268400	Active TSS	Psoas Muscle	Psoas
3	chr1:247266000-247269000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:247266200-247268400	Active TSS	HSMMtube	muscle
5	chr1:247266200-247268600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:247266200-247269000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:247266400-247268600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:247266400-247268600	Active TSS	Brain Angular Gyrus	brain
9	chr1:247266400-247268800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:247266400-247268800	Active TSS	Brain Hippocampus Middle	brain
11	chr1:247266600-247268400	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:247266600-247268400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:247266600-247268400	Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:247266600-247268400	Active TSS	Brain Substantia Nigra	brain
15	chr1:247266600-247268400	Active TSS	Fetal Brain Male	brain
16	chr1:247266600-247268600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:247266600-247268600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:247266600-247268600	Active TSS	Fetal Kidney	kidney
19	chr1:247266600-247268600	Active TSS	NHDF-Ad	bronchial
20	chr1:247266600-247268600	Active TSS	NHLF	lung
21	chr1:247266600-247268800	Active TSS	Colonic Mucosa	Colon
22	chr1:247266600-247268800	Active TSS	Ovary	ovary
23	chr1:247266600-247268800	Active TSS	Osteobl	bone
24	chr1:247266800-247268400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:247266800-247268400	Active TSS	Aorta	Aorta
26	chr1:247266800-247268600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:247266800-247268600	Active TSS	Pancreas	Pancrea
28	chr1:247266800-247268800	Active TSS	Brain Anterior Caudate	brain
29	chr1:247267200-247268600	Active TSS	Duodenum Mucosa	Duodenum
30	chr1:247267200-247268600	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr1:247267600-247268400	Active TSS	Brain Germinal Matrix	brain
32	chr1:247267800-247268400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:247267800-247268400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:247267800-247268400	Weak transcription	NH-A	brain
35	chr1:247268000-247268400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr1:247268000-247268400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:247268000-247268400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:247268000-247268400	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr1:247268000-247268400	Flanking Active TSS	Placenta	Placenta
40	chr1:247268000-247268400	Flanking Active TSS	Fetal Stomach	stomach
41	chr1:247268000-247268600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:247268000-247268600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:247268000-247268600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:247268000-247268600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:247268000-247268600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:247268000-247268600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:247268000-247268600	Bivalent Enhancer	Fetal Intestine Large	intestine
48	chr1:247268000-247268600	Enhancers	Spleen	Spleen
49	chr1:247268000-247268600	Flanking Active TSS	Dnd41	blood
50	chr1:247268000-247268800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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