Variant report

Variant	rs6843340
Chromosome Location	chr4:48619937-48619938
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	chr4:48617803..48619987-chr4:48625513..48627565,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10003273	0.83[AMR][1000 genomes]
rs10008265	0.83[AMR][1000 genomes]
rs10018344	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10029732	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10030853	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031777	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10049761	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10938534	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10938537	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11727343	0.92[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs11728565	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734019	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11737677	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11933919	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11945562	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12503599	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12506098	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12645501	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13108474	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13113370	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13119041	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs13119504	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13127730	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138269	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13141523	0.86[MKK][hapmap];0.80[YRI][hapmap]
rs13142540	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs13149083	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs13151534	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1507862	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1507865	0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1517674	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1554256	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1554258	0.83[AMR][1000 genomes]
rs1589107	0.81[AMR][1000 genomes]
rs1712768	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1712772	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17575720	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17656040	0.80[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17656076	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17656094	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1876469	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089503	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2102397	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2176460	0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2291474	0.81[JPT][hapmap]
rs2292231	0.83[AMR][1000 genomes]
rs2354312	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2354348	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28470767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2940324	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945330	0.82[EUR][1000 genomes]
rs3107022	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34558821	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34635008	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4536901	0.83[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4695391	0.83[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59686413	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62311296	0.84[EUR][1000 genomes]
rs6447640	0.82[EUR][1000 genomes]
rs6447645	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6447647	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447651	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6811148	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6814811	0.83[AMR][1000 genomes]
rs6818954	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6819159	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6829716	0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs6830848	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6836632	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6855022	0.83[EUR][1000 genomes]
rs6856448	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7654032	0.88[CEU][hapmap]
rs7654770	0.83[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs7657332	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7657698	1.00[JPT][hapmap]
rs7660206	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7661515	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7665209	0.81[ASW][hapmap];0.80[YRI][hapmap]
rs7667288	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7670939	0.83[EUR][1000 genomes]
rs7678379	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7679210	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7682859	0.82[EUR][1000 genomes]
rs7683398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7693461	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7697522	1.00[JPT][hapmap]
rs7697851	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs776584	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs776590	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs776591	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs776601	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796555	0.83[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937888	0.83[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs937889	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs952289	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9884546	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs992423	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
7	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6843340	OCIAD2	cis	lymphoblastoid	seeQTL
rs6843340	OCIAD2	cis	cerebellum	SCAN
rs6843340	SLC10A4	cis	lung	GTEx

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	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
6	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
7	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:48590600-48627600	Weak transcription	Fetal Brain Female	brain
9	chr4:48591200-48626600	Weak transcription	Ovary	ovary
10	chr4:48592200-48623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:48592400-48620800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:48594000-48622600	Weak transcription	Psoas Muscle	Psoas
13	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
14	chr4:48597000-48620800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:48598000-48623000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:48598200-48634800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:48599400-48620400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:48601000-48620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:48605200-48621400	Weak transcription	HMEC	breast
21	chr4:48605400-48622000	Weak transcription	Osteobl	bone
22	chr4:48605600-48620800	Weak transcription	NHDF-Ad	bronchial
23	chr4:48605600-48621000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:48606000-48626800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:48606200-48620800	Weak transcription	Fetal Heart	heart
26	chr4:48606800-48620600	Weak transcription	Right Atrium	heart
27	chr4:48606800-48622400	Weak transcription	Brain Angular Gyrus	brain
28	chr4:48606800-48624800	Weak transcription	Right Ventricle	heart
29	chr4:48606800-48637800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:48606800-48645000	Weak transcription	Gastric	stomach
31	chr4:48607000-48620000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:48607000-48625400	Weak transcription	Stomach Mucosa	stomach
33	chr4:48607400-48622400	Weak transcription	HepG2	liver
34	chr4:48608000-48625400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:48609600-48622000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr4:48609800-48637000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr4:48611400-48623800	Weak transcription	Fetal Brain Male	brain
38	chr4:48611800-48621200	Weak transcription	NHEK	skin
39	chr4:48613000-48624800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr4:48613400-48623000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:48614200-48622000	Weak transcription	Brain Anterior Caudate	brain
42	chr4:48614200-48622200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr4:48614400-48621800	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:48614400-48628800	Weak transcription	Fetal Kidney	kidney
45	chr4:48614600-48637000	Weak transcription	Small Intestine	intestine
46	chr4:48615600-48623400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:48616200-48625400	Strong transcription	Primary B cells from cord blood	blood
48	chr4:48616400-48625600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr4:48616600-48624200	Weak transcription	Brain Germinal Matrix	brain
50	chr4:48617200-48621800	Strong transcription	Fetal Intestine Large	intestine

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