Variant report

Variant	rs657030
Chromosome Location	chr6:161393311-161393312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161393062..161395612-chr6:161411949..161414335,2	K562	blood:
2	chr6:161393152..161396048-chr6:161411470..161414358,4	K562	blood:

Variant related genes	Relation type
ENSG00000085511	Chromatin interaction
ENSG00000272841	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs598919	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs614470	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs653571	0.89[ASN][1000 genomes]
rs653943	0.89[ASN][1000 genomes]
rs657484	0.89[ASN][1000 genomes]
rs673910	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs674333	0.87[ASN][1000 genomes]
rs675293	0.87[ASN][1000 genomes]
rs679814	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs679953	0.87[ASN][1000 genomes]
rs682216	0.86[ASN][1000 genomes]
rs788136	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	esv2422347	chr6:161211171-161442377	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs657030	FNDC1	cis	parietal	SCAN
rs657030	DYNLT1	cis	parietal	SCAN
rs657030	MAP3K4	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161372800-161394000	Weak transcription	Right Atrium	heart
2	chr6:161390800-161394200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:161391000-161393400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:161392200-161394400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:161392200-161394400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:161392200-161394400	Enhancers	NHDF-Ad	bronchial
7	chr6:161392200-161396400	Enhancers	HSMM	muscle
8	chr6:161392400-161394400	Weak transcription	Pancreas	Pancrea
9	chr6:161392400-161396400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:161392600-161393600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:161392600-161394000	Enhancers	Osteobl	bone
12	chr6:161392600-161395000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:161392600-161395800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:161392600-161396000	Enhancers	NH-A	brain
15	chr6:161392600-161396200	Enhancers	NHEK	skin
16	chr6:161392600-161396400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:161392800-161393600	Enhancers	HSMMtube	muscle
18	chr6:161392800-161396400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:161392800-161396400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:161392800-161396600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:161392800-161396600	Enhancers	HMEC	breast
22	chr6:161393000-161395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:161393000-161396400	Enhancers	Fetal Muscle Leg	muscle
24	chr6:161393000-161396400	Enhancers	NHLF	lung
25	chr6:161393200-161394200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:161393200-161394200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:161393200-161394600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:161393200-161395400	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:161393200-161397000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links