Variant report

Variant	rs12701873
Chromosome Location	chr7:41278362-41278363
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	chr7:41277967..41280193-chr7:41283626..41286439,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10951648	0.82[ASN][1000 genomes]
rs11762557	0.85[ASN][1000 genomes]
rs11765463	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11768019	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11768122	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12668579	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12701868	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12701870	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12701874	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12701875	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs12701876	0.81[ASN][1000 genomes]
rs13225532	0.81[EUR][1000 genomes]
rs13238496	0.81[ASN][1000 genomes]
rs13244372	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13311231	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1557928	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1557930	0.86[EUR][1000 genomes]
rs2051869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051871	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs255014	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs255017	0.80[EUR][1000 genomes]
rs34965184	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56215033	0.90[ASN][1000 genomes]
rs6951425	0.84[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs6955027	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6966153	0.90[EUR][1000 genomes]
rs6974692	0.82[ASN][1000 genomes]
rs7782143	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887989	chr7:41125447-41337044	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1028983	chr7:41165668-41635954	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv534465	chr7:41224437-41443498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3411047	chr7:41278282-41278812	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12701873	VPS41	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:41259400-41278400	Weak transcription	HSMM	muscle
2	chr7:41265000-41296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:41275800-41278600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr7:41277200-41279200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:41277200-41279200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:41277200-41279200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:41277200-41279400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:41277200-41279400	Enhancers	Hela-S3	cervix
9	chr7:41277200-41279400	Enhancers	NHDF-Ad	bronchial
10	chr7:41277400-41279200	Enhancers	NHEK	skin
11	chr7:41277400-41279400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:41277400-41279600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:41277400-41279600	Enhancers	HMEC	breast
14	chr7:41277400-41279600	Enhancers	Osteobl	bone
15	chr7:41277600-41279200	Enhancers	NHLF	lung
16	chr7:41277600-41279400	Enhancers	HUVEC	blood vessel
17	chr7:41277800-41278600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:41278000-41278400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:41278000-41279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:41278000-41279200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:41278200-41278600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links