Variant report

Variant	rs10924912
Chromosome Location	chr1:247263433-247263434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247249794..247251374-chr1:247261131..247263722,2	K562	blood:
2	chr1:247262370..247270931-chr1:247272613..247278774,19	MCF-7	breast:
3	chr1:247263178..247265761-chr1:247266072..247268985,2	MCF-7	breast:
4	chr1:247261271..247263933-chr1:247276366..247278097,2	K562	blood:

Variant related genes	Relation type
ENSG00000188295	Chromatin interaction
ENSG00000221953	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1007457	0.81[ASN][1000 genomes]
rs10754536	0.98[ASN][1000 genomes]
rs10802463	0.81[ASN][1000 genomes]
rs10802466	0.89[ASN][1000 genomes]
rs10802468	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10802469	0.98[ASN][1000 genomes]
rs10924907	0.89[ASN][1000 genomes]
rs10924909	0.94[ASN][1000 genomes]
rs10924910	0.95[ASN][1000 genomes]
rs10924914	0.98[ASN][1000 genomes]
rs10924915	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924917	0.97[ASN][1000 genomes]
rs10924919	0.97[ASN][1000 genomes]
rs10924924	0.83[ASN][1000 genomes]
rs11801681	0.85[ASN][1000 genomes]
rs12058648	0.81[ASN][1000 genomes]
rs12080836	0.97[ASN][1000 genomes]
rs12084753	0.94[ASN][1000 genomes]
rs12094740	0.94[ASN][1000 genomes]
rs12119007	0.82[ASN][1000 genomes]
rs12119918	0.98[ASN][1000 genomes]
rs12120049	0.83[ASN][1000 genomes]
rs12121338	0.82[ASN][1000 genomes]
rs12121363	0.85[ASN][1000 genomes]
rs12122715	0.81[ASN][1000 genomes]
rs12128943	0.85[ASN][1000 genomes]
rs12129591	0.81[ASN][1000 genomes]
rs12131094	0.82[ASN][1000 genomes]
rs12138526	0.97[ASN][1000 genomes]
rs12138686	0.95[ASN][1000 genomes]
rs12141797	0.94[ASN][1000 genomes]
rs12142274	0.82[ASN][1000 genomes]
rs12144733	0.94[ASN][1000 genomes]
rs12144854	0.85[ASN][1000 genomes]
rs12691533	0.95[ASN][1000 genomes]
rs12723583	0.84[ASN][1000 genomes]
rs13376442	0.94[ASN][1000 genomes]
rs1552988	0.94[ASN][1000 genomes]
rs2055190	0.92[ASN][1000 genomes]
rs2270616	0.97[ASN][1000 genomes]
rs2379192	0.91[ASN][1000 genomes]
rs2379193	0.94[ASN][1000 genomes]
rs2890101	0.92[ASN][1000 genomes]
rs2890102	0.94[ASN][1000 genomes]
rs2890103	0.94[ASN][1000 genomes]
rs2890104	0.94[ASN][1000 genomes]
rs2890105	0.94[ASN][1000 genomes]
rs2890106	0.94[ASN][1000 genomes]
rs34273666	0.94[ASN][1000 genomes]
rs34350972	0.94[ASN][1000 genomes]
rs34919391	0.82[ASN][1000 genomes]
rs35314391	0.94[ASN][1000 genomes]
rs35452630	0.94[ASN][1000 genomes]
rs35511369	0.94[ASN][1000 genomes]
rs3736325	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806269	0.91[ASN][1000 genomes]
rs3892246	0.94[ASN][1000 genomes]
rs3892516	0.94[ASN][1000 genomes]
rs41305955	0.91[ASN][1000 genomes]
rs4925692	0.89[ASN][1000 genomes]
rs4925701	0.83[ASN][1000 genomes]
rs4925702	0.85[ASN][1000 genomes]
rs4925703	0.83[ASN][1000 genomes]
rs4925704	0.85[ASN][1000 genomes]
rs4925711	0.82[ASN][1000 genomes]
rs4925715	0.82[ASN][1000 genomes]
rs55649449	0.88[ASN][1000 genomes]
rs57003817	0.94[ASN][1000 genomes]
rs60293371	0.94[ASN][1000 genomes]
rs60677310	0.94[ASN][1000 genomes]
rs60794525	0.94[ASN][1000 genomes]
rs6426217	0.85[ASN][1000 genomes]
rs6426218	0.92[ASN][1000 genomes]
rs6426220	0.87[ASN][1000 genomes]
rs6658298	0.92[ASN][1000 genomes]
rs6659256	0.94[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	0.89[ASN][1000 genomes]
rs6695894	0.81[ASN][1000 genomes]
rs6699898	0.97[ASN][1000 genomes]
rs6700824	0.82[ASN][1000 genomes]
rs6702419	0.92[ASN][1000 genomes]
rs7412787	0.92[ASN][1000 genomes]
rs7549674	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv533111	chr1:247200511-247264759	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	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
22	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
23	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
24	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
25	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
26	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
rs10924912	ZNF669	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247253200-247263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:247254000-247263600	Weak transcription	Placenta	Placenta
3	chr1:247254200-247266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:247258000-247263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:247258600-247263600	Strong transcription	Brain Germinal Matrix	brain
6	chr1:247259000-247263600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:247259000-247263600	Weak transcription	Fetal Heart	heart
8	chr1:247259400-247266000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:247259400-247266000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:247259600-247266000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr1:247259600-247266000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr1:247259600-247266600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:247259800-247265600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr1:247259800-247266200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:247260000-247265600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:247260000-247266200	ZNF genes & repeats	Liver	Liver
17	chr1:247260000-247266600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr1:247260200-247263800	Strong transcription	Dnd41	blood
19	chr1:247260200-247264200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:247260200-247265200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:247260200-247266000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:247260200-247266200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:247260200-247266400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr1:247260400-247263600	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:247260400-247263600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:247260400-247263600	Weak transcription	Stomach Mucosa	stomach
27	chr1:247260400-247265400	Strong transcription	Brain Anterior Caudate	brain
28	chr1:247260400-247265600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:247260400-247265800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
30	chr1:247260400-247265800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:247260400-247266600	ZNF genes & repeats	A549	lung
32	chr1:247260400-247266800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:247260600-247263600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:247260600-247264200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:247260600-247265800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:247260600-247266000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:247260800-247263600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:247260800-247263600	Weak transcription	Gastric	stomach
39	chr1:247260800-247263600	Weak transcription	Pancreas	Pancrea
40	chr1:247261000-247263600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:247261000-247263600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:247261000-247263800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:247261200-247263600	Weak transcription	Brain Substantia Nigra	brain
44	chr1:247261200-247263600	Weak transcription	Colonic Mucosa	Colon
45	chr1:247261200-247263600	Weak transcription	Fetal Brain Male	brain
46	chr1:247261200-247263600	Weak transcription	Right Ventricle	heart
47	chr1:247261200-247263600	Weak transcription	HSMMtube	muscle
48	chr1:247261200-247263800	Strong transcription	Fetal Brain Female	brain
49	chr1:247261400-247263600	Weak transcription	Brain Angular Gyrus	brain
50	chr1:247261400-247263600	Weak transcription	Brain Cingulate Gyrus	brain

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