Variant report

Variant	rs3779356
Chromosome Location	chr7:8298573-8298574
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	MXI1	chr7:8298200-8304061	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr7:8298278-8299758	SH-SY5Y	brain:	n/a	chr7:8298512-8298528 chr7:8298514-8298526 chr7:8298513-8298523
3	GATA2	chr7:8298348-8300011	SH-SY5Y	brain:	n/a	chr7:8298512-8298528 chr7:8298514-8298526 chr7:8298513-8298523
4	POLR2A	chr7:8295699-8298667	K562	blood:	n/a	n/a
5	EP300	chr7:8297240-8304935	SK-N-SH	brain:	n/a	chr7:8301242-8301256 chr7:8302651-8302665 chr7:8302093-8302106 chr7:8303194-8303204 chr7:8300605-8300614 chr7:8303165-8303175 chr7:8301853-8301862 chr7:8300606-8300615 chr7:8301597-8301613 chr7:8301595-8301604
6	EP300	chr7:8298267-8298762	SK-N-SH_RA	brain:	n/a	n/a
7	CEBPB	chr7:8298531-8298787	K562	blood:	n/a	n/a
8	EP300	chr7:8298311-8298728	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:8256019..8257810-chr7:8296899..8299475,2	MCF-7	breast:
2	chr7:8298365..8300507-chr7:8320944..8323781,2	K562	blood:
3	chr7:8297158..8299148-chr7:8314480..8317301,2	K562	blood:
4	chr7:8271962..8273684-chr7:8297680..8300078,2	K562	blood:

Variant related genes	Relation type
ENSG00000244239	TF binding region
ENSG00000229970	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1008038	0.89[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs10224736	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs10243615	0.90[EUR][1000 genomes]
rs10250445	0.86[EUR][1000 genomes]
rs11769978	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302551	0.88[ASN][1000 genomes]
rs2348906	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3779357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807801	0.95[ASN][1000 genomes]
rs3807802	0.95[ASN][1000 genomes]
rs3807803	0.95[ASN][1000 genomes]
rs3807804	0.95[ASN][1000 genomes]
rs3807806	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3807807	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3807808	0.94[ASN][1000 genomes]
rs3807809	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807810	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807811	0.88[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3823815	0.95[ASN][1000 genomes]
rs3823816	0.94[ASN][1000 genomes]
rs6463787	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6969962	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6970445	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv949024	chr7:8176301-8522495	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv1031226	chr7:8176311-8569811	Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv538724	chr7:8176311-8569811	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv887492	chr7:8177689-8513927	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv1026247	chr7:8178837-8527868	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv464305	chr7:8179655-8524707	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv606050	chr7:8179655-8524707	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv1020942	chr7:8179655-8524774	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv464307	chr7:8179846-8453313	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv606051	chr7:8179846-8453313	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
14	nsv1034583	chr7:8180210-8527868	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv1030373	chr7:8184961-8527868	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv949082	chr7:8189594-8494386	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	nsv948997	chr7:8189594-8522495	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
18	nsv915625	chr7:8201631-8554402	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv1033563	chr7:8222805-8512632	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
20	nsv1024586	chr7:8243829-8490078	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
21	nsv538725	chr7:8243829-8490078	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
22	nsv949715	chr7:8288705-8522495	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
23	nsv464308	chr7:8288705-8953858	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
24	nsv606054	chr7:8288705-8953858	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3779356	ICA1	cis	Liver	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8257200-8300200	Weak transcription	Fetal Stomach	stomach
2	chr7:8267600-8300400	Weak transcription	Fetal Intestine Small	intestine
3	chr7:8285200-8298800	Weak transcription	Fetal Intestine Large	intestine
4	chr7:8286200-8299000	Weak transcription	K562	blood
5	chr7:8289000-8300800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:8289800-8299800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:8289800-8300200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:8290000-8299400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:8290200-8299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:8294000-8300000	Weak transcription	Brain Angular Gyrus	brain
11	chr7:8294600-8300400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:8294800-8299000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:8294800-8300000	Weak transcription	Right Ventricle	heart
14	chr7:8294800-8300800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:8294800-8300800	Weak transcription	Gastric	stomach
16	chr7:8295000-8299200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:8295000-8299200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:8295600-8298600	Weak transcription	Stomach Mucosa	stomach
19	chr7:8296200-8300800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:8296400-8299000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:8296400-8300600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:8296400-8300600	Weak transcription	Placenta	Placenta
23	chr7:8296400-8300800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:8296600-8298800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:8296600-8299400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:8296600-8299400	Weak transcription	Right Atrium	heart
27	chr7:8296600-8300600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:8296600-8300800	Weak transcription	Lung	lung
29	chr7:8297200-8299000	Enhancers	Pancreas	Pancrea
30	chr7:8297400-8299800	Enhancers	Left Ventricle	heart
31	chr7:8298200-8300200	Enhancers	Fetal Heart	heart
32	chr7:8298200-8300400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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