Variant report

Variant	rs2294308
Chromosome Location	chr6:27483260-27483261
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	chr6:27482329..27484949-chr6:27859585..27861820,2	K562	blood:
2	chr6:27462160..27465243-chr6:27483150..27486620,3	K562	blood:

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1014227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1022486	0.82[YRI][hapmap]
rs1022515	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10452601	0.96[ASN][1000 genomes]
rs10484398	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10755644	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs10807020	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10807021	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10807024	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10807025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946913	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10946914	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10946919	0.90[ASN][1000 genomes]
rs10946920	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946921	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10946931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10946932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[ASN][1000 genomes]
rs10946933	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11968825	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11970336	0.92[ASN][1000 genomes]
rs12199110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12206045	0.96[ASN][1000 genomes]
rs12213598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215117	0.92[ASN][1000 genomes]
rs12524409	0.92[ASN][1000 genomes]
rs12529839	0.90[ASN][1000 genomes]
rs12662076	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13201443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13201965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13201985	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13212050	0.99[ASN][1000 genomes]
rs13215560	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217162	0.99[ASN][1000 genomes]
rs13217248	0.99[ASN][1000 genomes]
rs13220155	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1534937	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1883216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1883404	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs1883405	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1985818	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2015648	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2049944	0.92[ASN][1000 genomes]
rs2049945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2064219	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2076305	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2092120	0.88[ASN][1000 genomes]
rs2092121	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2092122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2103557	0.86[ASN][1000 genomes]
rs2142705	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2143062	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2179154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2205831	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2206250	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs2206251	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2206252	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2223463	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2223464	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2235252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2235254	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2272814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2272815	0.90[ASN][1000 genomes]
rs2272816	0.91[ASN][1000 genomes]
rs2294309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393929	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2393931	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs2893917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35394453	0.90[ASN][1000 genomes]
rs3734574	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs3734575	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4305708	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4358616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs4455661	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4478400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4504471	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4711147	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4711148	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4711153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4713086	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4713092	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs4713104	0.92[ASN][1000 genomes]
rs4713105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713106	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4713107	0.87[ASN][1000 genomes]
rs4713109	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62401365	0.92[ASN][1000 genomes]
rs6456774	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6456777	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6456778	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6456781	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6456785	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap]
rs6456786	0.90[ASN][1000 genomes]
rs6456788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6456789	0.92[ASN][1000 genomes]
rs6650992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6899950	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6903282	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904844	0.96[ASN][1000 genomes]
rs6904883	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6911865	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915934	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6918131	0.98[ASN][1000 genomes]
rs6918794	0.83[ASN][1000 genomes]
rs6920010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6920362	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6920408	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6920733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6921071	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6923108	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6923539	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6929812	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6931659	0.94[ASN][1000 genomes]
rs6933354	0.98[ASN][1000 genomes]
rs6934748	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6934985	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6936356	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6936539	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs6938943	1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs726830	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7509	0.86[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs764460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs764461	0.92[ASN][1000 genomes]
rs766092	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7741031	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7743443	0.92[ASN][1000 genomes]
rs7743465	0.92[ASN][1000 genomes]
rs7744110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7745380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7748366	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7750795	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7754411	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7754678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs7754724	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754977	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7756216	0.92[ASN][1000 genomes]
rs7756377	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7759001	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs7761989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7764070	0.92[ASN][1000 genomes]
rs7764634	0.87[ASN][1000 genomes]
rs7771590	0.99[ASN][1000 genomes]
rs7772160	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7774613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7776338	0.98[ASN][1000 genomes]
rs9357037	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs9461380	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9461386	0.86[ASN][1000 genomes]
rs9468101	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468111	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468115	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468117	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9468140	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468141	1.00[ASW][hapmap];0.95[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];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980960	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs980961	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs980962	1.00[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv462665	chr6:27458013-27547792	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv601203	chr6:27458013-27547792	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2294308	BTN3A2	cis	cerebellum	SCAN
rs2294308	ZSCAN23	cis	cerebellum	SCAN
rs2294308	ZNF391	cis	lung	GTEx
rs2294308	ZNF391	cis	cerebellum	SCAN
rs2294308	ZNF391	cis	Artery Tibial	GTEx
rs2294308	DCDC2	cis	cerebellum	SCAN
rs2294308	ZNF391	cis	Esophagus Muscularis	GTEx
rs2294308	ZNF391	cis	parietal	SCAN
rs2294308	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27482400-27483400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:27482400-27483400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:27482400-27483600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27482800-27485600	Weak transcription	K562	blood
5	chr6:27483000-27485800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:27483000-27486000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:27483200-27483400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:27483200-27485800	Weak transcription	Right Atrium	heart
9	chr6:27483200-27485800	Weak transcription	HMEC	breast
10	chr6:27483200-27486000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:27483200-27486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:27483200-27486200	Weak transcription	Ovary	ovary

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