Variant report

Variant	rs12121977
Chromosome Location	chr1:224599977-224599978
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:224599593-224600165	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:224599515-224600221	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:224598711-224600520	K562	blood:	n/a	n/a
4	POLR2A	chr1:224599892-224600515	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224595603..224601847-chr1:224621020..224623770,7	MCF-7	breast:

Variant related genes	Relation type
WDR26	TF binding region
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10495220	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10753465	0.80[YRI][hapmap]
rs10753467	0.80[YRI][hapmap]
rs10753468	0.80[YRI][hapmap]
rs10916607	0.84[YRI][hapmap]
rs10916614	0.80[YRI][hapmap]
rs1112556	0.83[ASN][1000 genomes]
rs12075578	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12120702	0.87[ASN][1000 genomes]
rs12124686	0.88[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128292	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12134167	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12140423	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1361618	0.83[ASN][1000 genomes]
rs2405023	0.83[ASN][1000 genomes]
rs4653588	0.83[ASN][1000 genomes]
rs4654037	0.84[YRI][hapmap]
rs56168737	0.83[ASN][1000 genomes]
rs6426121	0.80[YRI][hapmap]
rs6683524	0.84[EUR][1000 genomes]
rs6684878	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6693653	0.83[ASN][1000 genomes]
rs7517754	0.80[YRI][hapmap]
rs7529067	0.84[YRI][hapmap]
rs7529310	0.80[YRI][hapmap]
rs7536124	0.83[ASN][1000 genomes]
rs7542507	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:224572000-224617800	Strong transcription	Fetal Thymus	thymus
4	chr1:224572400-224601000	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:224572400-224617600	Strong transcription	Placenta	Placenta
6	chr1:224572600-224617600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:224572600-224617600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:224572600-224618400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:224573200-224618400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:224573200-224618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:224573600-224614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:224573600-224618200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:224573800-224615200	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:224574000-224601600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:224574000-224613600	Strong transcription	Adipose Nuclei	Adipose
16	chr1:224574600-224613600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:224575000-224607600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:224575200-224607600	Strong transcription	Fetal Intestine Large	intestine
19	chr1:224575200-224613800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr1:224575200-224616600	Strong transcription	Dnd41	blood
21	chr1:224575200-224616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:224576000-224601200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr1:224576200-224614000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:224576400-224614600	Strong transcription	HSMM	muscle
25	chr1:224577000-224617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:224578800-224614000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:224578800-224617200	Strong transcription	Liver	Liver
28	chr1:224579600-224617400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:224579800-224616000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:224581800-224615800	Strong transcription	K562	blood
31	chr1:224583200-224604200	Weak transcription	Fetal Heart	heart
32	chr1:224587000-224600000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:224589000-224611200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:224590400-224600400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:224590400-224612600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:224591200-224613000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:224591400-224607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:224591600-224600600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr1:224592400-224605400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:224592400-224605800	Weak transcription	Psoas Muscle	Psoas
41	chr1:224593400-224617000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:224593800-224605000	Weak transcription	Pancreas	Pancrea
43	chr1:224593800-224613600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:224595200-224600200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:224595400-224600000	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:224595400-224600200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:224595400-224613400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:224595400-224618000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:224595600-224600200	Strong transcription	Primary T cells from cord blood	blood
50	chr1:224595600-224600200	Strong transcription	Brain Angular Gyrus	brain

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