Variant report

Variant	rs4077495
Chromosome Location	chr3:48756512-48756513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48754698..48757669-chr3:48775875..48778896,4	K562	blood:
2	chr3:48755633..48757669-chr3:48777396..48780297,2	K562	blood:
3	chr3:48754717..48757980-chr3:48775781..48778989,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap]
rs1048940	0.84[CEU][hapmap]
rs10780033	1.00[CHD][hapmap]
rs10865952	0.95[ASN][1000 genomes]
rs11130176	1.00[CHD][hapmap]
rs11557629	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706203	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708022	0.84[AMR][1000 genomes]
rs11708786	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709092	0.80[AMR][1000 genomes]
rs11709246	0.84[AMR][1000 genomes]
rs11713694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs11715177	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715689	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11715713	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715835	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719291	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920534	1.00[CHD][hapmap]
rs11928552	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12107252	1.00[GIH][hapmap]
rs12107418	1.00[GIH][hapmap]
rs12493289	1.00[JPT][hapmap]
rs12493578	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12497850	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12715429	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060933	0.83[GIH][hapmap]
rs13063223	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063312	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13070798	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13073997	0.84[AMR][1000 genomes]
rs13074318	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs13084000	0.84[AMR][1000 genomes]
rs13087930	0.84[AMR][1000 genomes]
rs13090013	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094900	0.80[AMR][1000 genomes]
rs13316551	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319651	0.83[GIH][hapmap]
rs13324119	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13324142	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs13324950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352420	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17080289	1.00[GIH][hapmap]
rs17080319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006871	0.83[GIH][hapmap]
rs2276850	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs2276852	1.00[GIH][hapmap]
rs2286651	0.80[AMR][1000 genomes]
rs2286652	1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2302295	0.87[AMR][1000 genomes]
rs2310996	1.00[GIH][hapmap]
rs28452701	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2854394	0.83[GIH][hapmap]
rs28567949	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28657585	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28793701	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34037363	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs34096717	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34153629	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34477108	0.84[AMR][1000 genomes]
rs34509487	0.84[AMR][1000 genomes]
rs34577723	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733086	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3821876	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs4858798	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858828	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4858831	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4974079	1.00[CHD][hapmap]
rs4974085	1.00[CHD][hapmap]
rs4974087	1.00[CHD][hapmap]
rs56735597	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61137521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442130	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs67060340	0.80[AMR][1000 genomes]
rs67332931	0.84[AMR][1000 genomes]
rs6781283	0.83[GIH][hapmap]
rs6788650	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6791542	1.00[CHD][hapmap]
rs6792156	1.00[GIH][hapmap]
rs6792525	0.83[GIH][hapmap]
rs6806059	0.83[GIH][hapmap]
rs71324924	0.84[AMR][1000 genomes]
rs740787	1.00[GIH][hapmap]
rs7430501	1.00[CHD][hapmap]
rs7431710	1.00[CHD][hapmap]
rs7431857	1.00[CHD][hapmap]
rs7623023	1.00[CHD][hapmap]
rs7627404	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7631574	1.00[GIH][hapmap]
rs7633840	0.86[ASN][1000 genomes]
rs7647813	1.00[CHD][hapmap]
rs7649458	1.00[CHD][hapmap]
rs9311430	1.00[CHD][hapmap]
rs9311433	1.00[CHD][hapmap]
rs9311434	1.00[CHD][hapmap]
rs9682444	0.87[CHD][hapmap]
rs9755490	0.87[CHD][hapmap]
rs9810549	0.83[GIH][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	1.00[GIH][hapmap]
rs9812200	1.00[GIH][hapmap]
rs9830581	1.00[GIH][hapmap]
rs9834996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835307	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9836462	1.00[GIH][hapmap]
rs9837687	0.83[GIH][hapmap]
rs9841602	1.00[GIH][hapmap]
rs9843316	1.00[GIH][hapmap]
rs9848203	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850102	0.83[GIH][hapmap]
rs9854034	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868809	0.83[GIH][hapmap]
rs9869698	0.83[GIH][hapmap]
rs9871180	1.00[GIH][hapmap]
rs9873726	1.00[JPT][hapmap]
rs9876848	1.00[CHD][hapmap]
rs9877542	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882962	0.83[GIH][hapmap]

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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4077495	C3orf62	cis	parietal	SCAN
rs4077495	WDR6	cis	lymphoblastoid	seeQTL
rs4077495	ALAS1	cis	cerebellum	SCAN
rs4077495	WDR6	cis	parietal	SCAN
rs4077495	USP4	cis	multi-tissue	Pritchard
rs4077495	WDR6	cis	cerebellum	SCAN
rs4077495	CSPG5	cis	parietal	SCAN
rs4077495	NCKIPSD	cis	parietal	SCAN
rs4077495	RNF123	cis	parietal	SCAN
rs4077495	WDR6	cis	multi-tissue	Pritchard
rs4077495	LRRC2	cis	cerebellum	SCAN
rs4077495	C3orf62	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48754800-48759000	Weak transcription	Gastric	stomach
2	chr3:48755200-48757600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:48755200-48758000	Weak transcription	Fetal Lung	lung
4	chr3:48755200-48759000	Weak transcription	Fetal Kidney	kidney
5	chr3:48755200-48760000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:48755200-48760200	Weak transcription	Small Intestine	intestine
7	chr3:48755400-48756800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:48755400-48757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:48755400-48757600	Weak transcription	Spleen	Spleen
10	chr3:48755400-48758000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:48755400-48758000	Weak transcription	Stomach Mucosa	stomach
12	chr3:48755400-48759000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:48755400-48760200	Weak transcription	Colonic Mucosa	Colon
14	chr3:48755400-48760200	Weak transcription	A549	lung
15	chr3:48755400-48760400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:48755600-48760200	Weak transcription	K562	blood
17	chr3:48755800-48756800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:48756000-48757000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:48756000-48759000	Weak transcription	Pancreas	Pancrea
20	chr3:48756200-48758800	Weak transcription	HepG2	liver

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