Variant report

Variant	rs4680298
Chromosome Location	chr3:156387115-156387116
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156364332..156366414-chr3:156385028..156387855,2	MCF-7	breast:
2	chr3:156377877..156380030-chr3:156386212..156388367,2	MCF-7	breast:
3	chr3:156384119..156388903-chr3:156389462..156394403,8	MCF-7	breast:
4	chr3:156318948..156323685-chr3:156384396..156387913,5	K562	blood:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs11710516	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11926558	0.85[AMR][1000 genomes]
rs13073605	0.85[AMR][1000 genomes]
rs13097957	0.83[CHD][hapmap]
rs1355280	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1397194	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1397195	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1430412	0.83[CHD][hapmap]
rs1510269	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1510270	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs168245	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16826858	0.83[CHD][hapmap]
rs168295	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs180746	0.83[EUR][1000 genomes]
rs180747	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs182935	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs182936	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs184677	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1858229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs186928	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs193198	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs193423	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2054881	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2129909	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2136691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs237245	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs237246	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2665390	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap]
rs343991	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs343992	0.83[CHD][hapmap]
rs343995	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343996	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343997	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs343998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344000	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344001	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs344008	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs344009	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344010	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344012	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344013	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344014	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344015	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs344016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344017	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344023	0.83[EUR][1000 genomes]
rs344029	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344032	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344047	0.83[EUR][1000 genomes]
rs344048	0.83[EUR][1000 genomes]
rs344049	0.83[EUR][1000 genomes]
rs344050	0.83[EUR][1000 genomes]
rs344052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344053	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344054	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344059	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs344060	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344061	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344062	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes]
rs344064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344065	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344066	1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344068	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344069	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344070	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs344076	0.83[CHD][hapmap]
rs344081	0.83[CHD][hapmap]
rs344088	0.83[CHD][hapmap]
rs344090	0.83[CHD][hapmap]
rs345987	0.83[AMR][1000 genomes]
rs414683	0.83[CHD][hapmap]
rs419287	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs427384	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4429586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4679784	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680296	0.85[AMR][1000 genomes]
rs4680297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491423	0.83[CHD][hapmap]
rs5012666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441088	0.83[LWK][hapmap];0.85[AMR][1000 genomes]
rs6441089	1.00[AMR][1000 genomes]
rs6441092	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441095	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618306	0.83[CHD][hapmap]
rs7636366	0.85[AMR][1000 genomes]
rs7640593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs978109	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9833951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841047	0.85[AMR][1000 genomes]
rs9847692	0.83[CHD][hapmap]
rs985854	0.85[AMR][1000 genomes]
rs9877043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4680298	C2CD4B	trans	brain	seeQTL
rs4680298	CSF3	trans	brain	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156382400-156388000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr3:156382600-156391600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:156383000-156391400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:156383200-156388000	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr3:156383600-156387800	Weak transcription	HUVEC	blood vessel
6	chr3:156383600-156390600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:156384200-156391400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:156385600-156390600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:156386000-156387200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:156386200-156391600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:156386400-156390800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:156386400-156391200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:156386400-156391200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:156386400-156391200	Weak transcription	NHEK	skin
16	chr3:156386400-156391400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:156386400-156391400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:156386400-156391400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:156386400-156391400	Weak transcription	Fetal Intestine Small	intestine
20	chr3:156386400-156391600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:156386400-156391600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:156386400-156391600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:156386600-156388600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:156386600-156389200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:156386600-156390600	Weak transcription	HepG2	liver
26	chr3:156386600-156391200	Weak transcription	Liver	Liver
27	chr3:156386600-156391400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:156386600-156391400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:156386600-156391400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:156386600-156391400	Weak transcription	A549	lung
31	chr3:156386600-156391400	Weak transcription	HMEC	breast
32	chr3:156386600-156391600	Weak transcription	Fetal Lung	lung
33	chr3:156386800-156387200	Weak transcription	Small Intestine	intestine
34	chr3:156386800-156387400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156386800-156387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:156386800-156391200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:156386800-156391200	Weak transcription	GM12878-XiMat	blood
38	chr3:156386800-156391200	Weak transcription	K562	blood
39	chr3:156386800-156391600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:156386800-156391600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:156386800-156391600	Weak transcription	Fetal Intestine Large	intestine
42	chr3:156386800-156391600	Weak transcription	NHLF	lung
43	chr3:156387000-156387800	Weak transcription	Stomach Mucosa	stomach
44	chr3:156387000-156391000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:156387000-156391200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:156387000-156391200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:156387000-156391200	Weak transcription	Hela-S3	cervix
48	chr3:156387000-156391400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:156387000-156391400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:156387000-156391400	Weak transcription	Rectal Mucosa Donor 29	rectum

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