Variant report

Variant	rs1961746
Chromosome Location	chr2:56374649-56374650
allele	A/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	SIN3AK20	chr2:56374599-56375169	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:56374591-56374969	T-47D	breast:	n/a	n/a
3	NR2F2	chr2:56374636-56375058	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:56374590-56375022	T-47D	breast:	n/a	n/a
5	GATA3	chr2:56374531-56375141	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000271894	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10490394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1432555	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17189988	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2021413	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4672087	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4672090	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4672092	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55794437	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55809599	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6722720	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6739384	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6743269	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751834	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72798994	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72798995	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72801106	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72801108	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72801110	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72801117	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72801145	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv34703	chr2:56272949-56382181	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874164	chr2:56280428-56388746	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv874165	chr2:56280428-56393918	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv9824	chr2:56282176-56392083	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv874167	chr2:56284418-56388746	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv457952	chr2:56292883-56388746	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv582031	chr2:56292883-56388746	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv874168	chr2:56363377-56393918	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56350600-56375000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:56370400-56377600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:56370600-56375000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:56372200-56375400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:56372600-56375600	Enhancers	K562	blood
6	chr2:56373800-56378400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:56374600-56376800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:56374600-56378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links