Variant report

Variant	rs9874866
Chromosome Location	chr3:156538670-156538671
allele	A/G
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	BHLHE40	chr3:156538542-156538742	A549	lung:	n/a	n/a
2	RUNX3	chr3:156537851-156538715	GM12878	blood:	n/a	chr3:156538304-156538313
3	NFIC	chr3:156537804-156538755	GM12878	blood:	n/a	chr3:156538654-156538682
4	POLR2A	chr3:156538625-156539012	IMR90	lung:	n/a	n/a
5	EBF1	chr3:156538496-156538796	GM12878	blood:	n/a	chr3:156538645-156538654 chr3:156538644-156538654 chr3:156538643-156538654
6	POLR2A	chr3:156538567-156538796	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:156538522-156538834	Raji	blood:	n/a	n/a
8	TBL1XR1	chr3:156538112-156538706	GM12878	blood:	n/a	n/a
9	EP300	chr3:156537963-156538706	GM12878	blood:	n/a	n/a
10	EBF1	chr3:156538290-156538856	GM12878	blood:	n/a	chr3:156538645-156538654 chr3:156538644-156538654 chr3:156538643-156538654
11	POU2F2	chr3:156538095-156538713	GM12878	blood:	n/a	chr3:156538350-156538362 chr3:156538351-156538361 chr3:156538344-156538365 chr3:156538349-156538362 chr3:156538348-156538362 chr3:156538351-156538361 chr3:156538609-156538622 chr3:156538351-156538360
12	RUNX3	chr3:156537947-156538743	GM12878	blood:	n/a	chr3:156538304-156538313
13	EP300	chr3:156538266-156538753	GM12878	blood:	n/a	n/a
14	WRNIP1	chr3:156538640-156538772	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156537501..156540468-chr3:156557246..156559245,2	K562	blood:
2	chr3:156536226..156539045-chr3:156559314..156561294,2	MCF-7	breast:
3	chr3:156392338..156393905-chr3:156537590..156540285,2	MCF-7	breast:
4	chr14:55513055..55515662-chr3:156536623..156538871,2	MCF-7	breast:
5	chr3:156537180..156540050-chr3:156547950..156549740,2	K562	blood:

Variant related genes	Relation type
LINC00886	TF binding region
LEKR1	TF binding region
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12497539	1.00[CEU][hapmap]
rs1430410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2653817	0.83[YRI][hapmap]
rs344071	0.81[YRI][hapmap]
rs344072	0.82[YRI][hapmap]
rs344074	0.81[YRI][hapmap]
rs6776157	0.85[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7641929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9820830	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs9858861	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9874866	Hs.54543	cis	multi-tissue	Pritchard
rs9874866		cis	Lymphoblastoid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156535400-156538800	Weak transcription	Lung	lung
2	chr3:156535400-156539000	Enhancers	HSMM	muscle
3	chr3:156535400-156539200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:156535400-156543400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:156535600-156538800	Enhancers	HSMMtube	muscle
6	chr3:156535600-156538800	Enhancers	NHDF-Ad	bronchial
7	chr3:156535600-156539000	Enhancers	HMEC	breast
8	chr3:156535600-156539000	Enhancers	HUVEC	blood vessel
9	chr3:156536200-156538800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:156536200-156539000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:156536200-156543200	Weak transcription	Fetal Kidney	kidney
12	chr3:156536400-156538800	Enhancers	NHEK	skin
13	chr3:156536400-156539000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:156536400-156539000	Enhancers	Hela-S3	cervix
15	chr3:156536400-156539000	Enhancers	Osteobl	bone
16	chr3:156536400-156542400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:156536400-156542400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:156536400-156543000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:156536400-156543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:156536400-156543200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:156536400-156543200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:156536400-156543200	Weak transcription	Thymus	Thymus
23	chr3:156536600-156541600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:156536800-156541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:156537000-156539000	Enhancers	NH-A	brain
26	chr3:156537000-156540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:156537000-156540400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:156537000-156541800	Weak transcription	Fetal Intestine Small	intestine
29	chr3:156537000-156543200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:156537000-156543400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:156537000-156543400	Weak transcription	Liver	Liver
32	chr3:156537000-156543600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:156537000-156543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:156537200-156538800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:156537200-156541000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:156537200-156542600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:156537600-156538800	Enhancers	A549	lung
38	chr3:156537600-156542400	Weak transcription	K562	blood
39	chr3:156538000-156539000	Enhancers	Stomach Mucosa	stomach
40	chr3:156538000-156543400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:156538200-156538800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:156538600-156539200	Enhancers	GM12878-XiMat	blood
43	chr3:156538600-156540800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:156538600-156543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:156538600-156543400	Weak transcription	NHLF	lung

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