Variant report

Variant	rs3107022
Chromosome Location	chr4:48617387-48617388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48615973..48618309-chr4:48625425..48627835,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10018344	0.85[EUR][1000 genomes]
rs10029732	0.85[EUR][1000 genomes]
rs10030853	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10031777	0.85[EUR][1000 genomes]
rs10049761	0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10938534	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10938537	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11727343	0.82[CEU][hapmap]
rs11728565	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11734019	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737677	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11933919	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11945562	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs12503599	0.84[EUR][1000 genomes]
rs12506098	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13108474	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119041	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs13127730	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13138269	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13142540	1.00[JPT][hapmap]
rs13151534	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1507862	0.85[EUR][1000 genomes]
rs1507865	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1517674	1.00[JPT][hapmap]
rs1554256	0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs16861510	0.83[YRI][hapmap]
rs1702798	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1712767	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1712768	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1712772	0.82[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17575720	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17656010	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17656040	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17656076	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17656094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1876469	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089503	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2102397	0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs2176460	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2291474	0.81[JPT][hapmap]
rs2354348	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2354938	0.82[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs28470767	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28733443	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2940324	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945330	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34558821	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34635008	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4536901	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4695391	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695397	0.82[EUR][1000 genomes]
rs4695400	0.80[AFR][1000 genomes]
rs4695401	0.80[AFR][1000 genomes]
rs59686413	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62311296	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6447640	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6447645	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447647	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447655	0.80[AFR][1000 genomes]
rs6811148	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6819159	0.85[EUR][1000 genomes]
rs6829144	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6829716	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6830848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6836632	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs6843340	0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6855022	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6856448	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7654770	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7657332	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7657698	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7660206	0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7661515	0.85[EUR][1000 genomes]
rs7665209	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs7667288	0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs7678379	0.87[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs7679210	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7680280	0.80[EUR][1000 genomes]
rs7683398	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7693461	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7697522	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7697851	0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs776584	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs776588	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs776590	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs776591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs776601	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs776602	0.85[YRI][hapmap]
rs796555	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs937888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs937889	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs952289	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs9790336	0.80[AFR][1000 genomes]
rs9884546	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs992423	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv966557	chr4:48577320-48618907	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3107022	SLC10A4	cis	lung	GTEx
rs3107022	OCIAD2	cis	cerebellum	SCAN
rs3107022	OCIAD2	cis	lymphoblastoid	seeQTL
rs3107022	OCIAD2	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
2	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
7	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
8	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:48588800-48619600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:48590600-48627600	Weak transcription	Fetal Brain Female	brain
11	chr4:48590800-48619600	Weak transcription	Fetal Stomach	stomach
12	chr4:48590800-48619600	Weak transcription	Lung	lung
13	chr4:48591000-48618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:48591000-48619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:48591200-48626600	Weak transcription	Ovary	ovary
16	chr4:48591400-48619600	Weak transcription	Fetal Muscle Leg	muscle
17	chr4:48591800-48619000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:48592200-48623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:48592400-48620800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:48592600-48619600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:48594000-48619600	Weak transcription	Aorta	Aorta
22	chr4:48594000-48622600	Weak transcription	Psoas Muscle	Psoas
23	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
24	chr4:48596800-48619000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:48597000-48619400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:48597000-48620800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:48597400-48619600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:48597600-48618600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:48598000-48623000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:48598200-48634800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:48598600-48618800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:48598600-48619600	Weak transcription	GM12878-XiMat	blood
34	chr4:48598800-48619200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:48599400-48620400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:48601000-48620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:48601800-48619800	Weak transcription	Placenta	Placenta
38	chr4:48602200-48619400	Weak transcription	Thymus	Thymus
39	chr4:48605000-48617800	Weak transcription	NHLF	lung
40	chr4:48605200-48621400	Weak transcription	HMEC	breast
41	chr4:48605400-48618600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:48605400-48619800	Weak transcription	NH-A	brain
43	chr4:48605400-48622000	Weak transcription	Osteobl	bone
44	chr4:48605600-48620800	Weak transcription	NHDF-Ad	bronchial
45	chr4:48605600-48621000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:48606000-48626800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:48606200-48620800	Weak transcription	Fetal Heart	heart
48	chr4:48606400-48619600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:48606600-48618600	Weak transcription	Colonic Mucosa	Colon
50	chr4:48606600-48619600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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