Variant report

Variant	rs6456718
Chromosome Location	chr6:26351937-26351938
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26350529..26353058-chr6:26354416..26356563,2	K562	blood:
2	chr6:26351127..26352720-chr6:26382336..26385327,2	K562	blood:
3	chr1:17222072..17224236-chr6:26350716..26352236,2	K562	blood:
4	chr1:17221559..17223078-chr6:26350716..26352216,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124508	Chromatin interaction
ENSG00000207005	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12203176	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205476	0.83[ASN][1000 genomes]
rs12206621	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664899	0.83[ASN][1000 genomes]
rs14232	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17537465	0.83[ASN][1000 genomes]
rs35183513	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712982	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55827419	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55984635	0.89[AFR][1000 genomes];0.96[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	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456716	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914931	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72836457	0.88[AFR][1000 genomes];0.96[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]
rs9104	0.80[EUR][1000 genomes]
rs9461245	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467716	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467717	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467718	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467723	0.85[EUR][1000 genomes]
rs9688949	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	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
9	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
10	esv3488794	chr6:26342723-26352721	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	esv3488795	chr6:26343123-26352621	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv2432404	chr6:26343226-26352258	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6456718	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs6456718	BTN3A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26343200-26352400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:26348000-26355600	Weak transcription	Fetal Thymus	thymus
3	chr6:26348600-26354800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:26348800-26354400	Weak transcription	Fetal Intestine Small	intestine
5	chr6:26349000-26354200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:26350200-26353000	Enhancers	Hela-S3	cervix
7	chr6:26350200-26353200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:26350400-26352200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:26350400-26352400	Enhancers	NH-A	brain
10	chr6:26350600-26352200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:26350600-26352200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:26350600-26352600	Enhancers	NHLF	lung
13	chr6:26350800-26352600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:26350800-26352600	Enhancers	Osteobl	bone
15	chr6:26350800-26354600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:26351000-26352000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:26351000-26352600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:26351000-26352600	Enhancers	HMEC	breast
19	chr6:26351000-26352600	Enhancers	NHEK	skin
20	chr6:26351000-26352800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:26351000-26352800	Enhancers	HSMM	muscle
22	chr6:26351000-26353000	Enhancers	NHDF-Ad	bronchial
23	chr6:26351200-26352400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:26351200-26352600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:26351200-26352600	Enhancers	HUVEC	blood vessel
26	chr6:26351200-26353400	Enhancers	K562	blood
27	chr6:26351200-26354400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:26351400-26352400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:26351400-26353200	Enhancers	HepG2	liver
30	chr6:26351600-26352000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:26351600-26352000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:26351600-26352000	Flanking Active TSS	A549	lung
33	chr6:26351600-26352200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:26351600-26355600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:26351800-26352000	Enhancers	H9 Cell Line	embryonic stem cell
36	chr6:26351800-26352200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:26351800-26353000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:26351800-26353200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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