Variant report

Variant	rs7760906
Chromosome Location	chr6:25374754-25374755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25373645..25375161-chr6:25378953..25381156,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1013045	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209305	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173289	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12210416	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs13211247	0.83[ASN][1000 genomes]
rs13217807	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1556043	0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs169978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs177333	0.85[ASN][1000 genomes]
rs215009	0.89[ASN][1000 genomes]
rs215013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs215014	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690059	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2744234	0.86[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2744237	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35361710	0.85[ASN][1000 genomes]
rs4712921	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712922	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456678	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6913927	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6933921	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs760864	0.93[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7760906	BTN3A2	cis	cerebellum	SCAN
rs7760906	OR2B2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25368000-25378400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:25368200-25375400	Weak transcription	Primary B cells from cord blood	blood
3	chr6:25370400-25377200	Weak transcription	Right Atrium	heart
4	chr6:25370400-25378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:25370800-25377200	Weak transcription	Gastric	stomach
6	chr6:25370800-25388800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:25371000-25377000	Weak transcription	Pancreas	Pancrea
8	chr6:25371000-25377400	Weak transcription	Aorta	Aorta
9	chr6:25371400-25378400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:25371600-25377000	Weak transcription	Fetal Intestine Small	intestine
11	chr6:25371800-25377400	Weak transcription	Thymus	Thymus
12	chr6:25372000-25375600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:25372400-25375200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:25373800-25374800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:25373800-25377600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:25374000-25376000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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