Variant report

Variant	rs9461406
Chromosome Location	chr6:27719764-27719765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27218569..27220460-chr6:27719318..27721940,3	MCF-7	breast:
2	chr6:27144211..27146855-chr6:27719701..27721733,2	K562	blood:
3	chr6:27713706..27716261-chr6:27717105..27720222,3	K562	blood:
4	chr6:27615823..27619826-chr6:27718831..27721663,4	K562	blood:
5	chr6:27438716..27440637-chr6:27717595..27720128,2	K562	blood:
6	chr6:27129261..27130116-chr6:27719696..27720311,2	MCF-7	breast:
7	chr6:27615823..27619826-chr6:27719510..27721663,4	K562	blood:
8	chr6:27716568..27718796-chr6:27718856..27720931,2	K562	blood:
9	chr6:27263338..27266126-chr6:27718637..27721483,2	K562	blood:
10	chr6:27713445..27716447-chr6:27717145..27720805,5	K562	blood:
11	chr6:27558583..27561214-chr6:27719565..27721812,2	K562	blood:
12	chr6:27719316..27720224-chr6:27760005..27760520,2	K562	blood:
13	chr6:27704721..27706812-chr6:27718654..27720926,2	K562	blood:
14	chr6:27661813..27662703-chr6:27719579..27720188,2	MCF-7	breast:
15	chr6:27113190..27116258-chr6:27719531..27723256,5	K562	blood:
16	chr6:27486493..27487200-chr6:27719731..27720643,4	K562	blood:
17	chr6:27686786..27690624-chr6:27717358..27721129,5	K562	blood:
18	chr6:27719685..27721542-chr6:27859391..27861101,2	MCF-7	breast:
19	chr6:27520849..27522507-chr6:27719657..27722145,3	K562	blood:
20	chr6:27661606..27663243-chr6:27719625..27721150,2	K562	blood:
21	chr6:27510934..27513659-chr6:27719612..27722020,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000216915	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10214440	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10484401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1139226	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13215072	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs169262	0.83[ASN][1000 genomes]
rs1985099	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200468	0.86[ASN][1000 genomes]
rs200475	0.80[ASN][1000 genomes]
rs200476	0.83[ASN][1000 genomes]
rs200502	0.90[CEU][hapmap]
rs200956	0.83[CHD][hapmap]
rs200969	0.83[CHD][hapmap]
rs200991	0.83[CHD][hapmap]
rs2056925	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2092075	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2179095	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2394000	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394002	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893929	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2893930	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2893931	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34752872	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35069907	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35957409	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4140646	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4711163	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713118	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713121	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs573179	0.83[CHD][hapmap]
rs6901520	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6902689	0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6914924	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922574	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930992	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs742046	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs742047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs760587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756968	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759217	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760523	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7772027	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7773070	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776351	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283880	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283881	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283882	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9283883	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295740	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9295742	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295743	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9348774	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9348775	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357045	0.94[ASN][1000 genomes]
rs9366700	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366702	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368528	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368529	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9368530	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380010	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380011	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380012	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393847	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393848	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461401	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461405	0.95[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468195	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9468199	0.86[ASN][1000 genomes]
rs9468200	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468201	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468203	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468204	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468214	0.90[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468217	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468219	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9468223	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9461406	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9461406	BTN2A1	cis	cerebellum	SCAN
rs9461406	HIST1H3C	cis	cerebellum	SCAN
rs9461406	BTN2A1	cis	parietal	SCAN
rs9461406	OR2B8P	cis	Thyroid	GTEx
rs9461406	ZKSCAN3	cis	parietal	SCAN
rs9461406	AL022393.7	cis	Muscle Skeletal	GTEx
rs9461406	BTN3A3	cis	cerebellum	SCAN
rs9461406	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9461406	BTN3A3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27719000-27719800	Enhancers	NHEK	skin
2	chr6:27719200-27719800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:27719400-27719800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:27719400-27720200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:27719400-27720200	Enhancers	Osteobl	bone
6	chr6:27719600-27719800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:27719600-27720000	Enhancers	GM12878-XiMat	blood
8	chr6:27719600-27720000	Enhancers	Hela-S3	cervix
9	chr6:27719600-27720200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:27719600-27720200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:27719600-27720200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:27719600-27720200	Enhancers	Stomach Mucosa	stomach
13	chr6:27719600-27720200	Flanking Active TSS	Dnd41	blood
14	chr6:27719600-27720200	Flanking Active TSS	HepG2	liver
15	chr6:27719600-27720200	Enhancers	HMEC	breast

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