Variant report

Variant	rs9467717
Chromosome Location	chr6:26348457-26348458
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26346422..26348741-chr6:26456867..26458564,3	K562	blood:
2	chr6:26346737..26349010-chr6:26483438..26485200,2	K562	blood:

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1131936	0.83[CEU][hapmap]
rs12203176	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205476	0.83[ASN][1000 genomes]
rs12206621	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208788	0.83[CEU][hapmap]
rs12664899	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs14232	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17537465	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs35183513	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3902051	0.83[CEU][hapmap]
rs4711108	0.83[CEU][hapmap]
rs4712982	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712986	0.83[CEU][hapmap]
rs4712988	0.83[CEU][hapmap]
rs55827419	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55984635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56380525	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456715	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456716	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456718	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914931	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72836457	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72836479	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841510	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72841540	0.83[ASN][1000 genomes]
rs7355	0.83[CEU][hapmap]
rs7356849	0.83[CEU][hapmap]
rs9104	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9461245	1.00[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467716	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467718	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467721	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467723	0.85[EUR][1000 genomes]
rs9688949	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
7	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv3521788	chr6:26334022-26356973	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3521789	chr6:26334022-26356973	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv601174	chr6:26341301-26350938	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	esv3488794	chr6:26342723-26352721	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	esv3488795	chr6:26343123-26352621	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	esv2432404	chr6:26343226-26352258	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	esv2398249	chr6:26343632-26351761	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv3472306	chr6:26343692-26351682	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	esv3488796	chr6:26343714-26351683	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	esv3488800	chr6:26343723-26351656	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	esv3488798	chr6:26343740-26351609	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	esv3472307	chr6:26343745-26351652	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
21	esv3472305	chr6:26343760-26351606	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
22	esv3488802	chr6:26343764-26351614	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	esv3488801	chr6:26343767-26351620	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	esv3389171	chr6:26343787-26351590	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	esv3472309	chr6:26343812-26351575	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
26	esv3488799	chr6:26343822-26351574	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	esv3472310	chr6:26343826-26351572	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
28	esv3488803	chr6:26343826-26351572	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	esv12557	chr6:26343849-26351580	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
30	nsv601175	chr6:26344975-26350565	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	nsv601176	chr6:26344975-26350778	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
32	nsv601177	chr6:26344975-26350938	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
33	nsv601178	chr6:26344975-26351325	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
34	nsv601180	chr6:26345141-26349025	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
35	nsv601181	chr6:26345141-26350778	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
36	nsv601182	chr6:26345141-26351325	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
37	nsv514347	chr6:26345241-26351203	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
38	nsv601183	chr6:26346175-26351325	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9467717	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL
rs9467717	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26342400-26351800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:26342600-26350200	Weak transcription	Hela-S3	cervix
3	chr6:26342800-26349800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26343000-26350800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:26343200-26348600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:26343200-26352400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:26344000-26348600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:26344200-26349000	Enhancers	K562	blood
9	chr6:26345000-26350400	Enhancers	HepG2	liver
10	chr6:26347600-26349000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:26347800-26348800	Enhancers	Fetal Intestine Small	intestine
12	chr6:26347800-26349000	Enhancers	Fetal Intestine Large	intestine
13	chr6:26348000-26348800	Enhancers	A549	lung
14	chr6:26348000-26349000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:26348000-26355600	Weak transcription	Fetal Thymus	thymus
16	chr6:26348200-26348600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:26348200-26348800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:26348200-26349000	Enhancers	Stomach Mucosa	stomach
19	chr6:26348200-26349200	Enhancers	NHEK	skin
20	chr6:26348200-26351800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:26348400-26348600	Enhancers	Duodenum Mucosa	Duodenum
22	chr6:26348400-26350600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links