Variant report

Variant	rs6674050
Chromosome Location	chr1:85516174-85516175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr1:85515999-85517129	HEK293	kidney:	n/a	chr1:85516570-85516584

Variant related genes	Relation type
MCOLN3	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12119445	0.83[CEU][hapmap]
rs12730329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12755226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17371526	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34407588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34422870	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34443659	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34482655	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35569266	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4301650	0.82[EUR][1000 genomes]
rs4907019	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907117	1.00[CEU][hapmap]
rs55997821	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56015101	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56110958	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6576739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66631937	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67628430	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72720544	0.91[EUR][1000 genomes];0.92[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	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674050	MCOLN2	cis	multi-tissue	Pritchard
rs6674050	CLCA3P	cis	parietal	SCAN
rs6674050	MCOLN2	cis	lymphoblastoid	seeQTL
rs6674050	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85514600-85516200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:85514600-85516600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
3	chr1:85514600-85516800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
4	chr1:85514600-85517600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:85514800-85516400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
6	chr1:85514800-85527400	Weak transcription	Aorta	Aorta
7	chr1:85515200-85516200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:85515200-85517600	Enhancers	Dnd41	blood
9	chr1:85515600-85516400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
10	chr1:85515600-85517000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr1:85515600-85517200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:85515800-85516200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr1:85515800-85516200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
14	chr1:85515800-85516200	Enhancers	Primary T cells from cord blood	blood
15	chr1:85515800-85516400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr1:85515800-85516600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr1:85515800-85517000	Enhancers	Fetal Intestine Small	intestine
18	chr1:85515800-85517400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:85515800-85523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:85516000-85516600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr1:85516000-85517000	Enhancers	Fetal Intestine Large	intestine
22	chr1:85516000-85517400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links