Variant report

Variant	rs2231170
Chromosome Location	chr7:100253274-100253275
allele	A/G
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	RFX5	chr7:100253117-100254706	SK-N-SH	brain:	n/a	chr7:100254236-100254250 chr7:100254117-100254126
2	REST	chr7:100253143-100254438	A549	lung:	n/a	chr7:100254148-100254161 chr7:100253640-100253654 chr7:100253625-100253638
3	REST	chr7:100253107-100254468	SK-N-SH	brain:	n/a	chr7:100254148-100254161 chr7:100253640-100253654 chr7:100253625-100253638
4	REST	chr7:100253180-100254388	H1-hESC	embryonic stem cell:	n/a	chr7:100254148-100254161 chr7:100253640-100253654 chr7:100253625-100253638
5	MXI1	chr7:100252893-100254996	SK-N-SH	brain:	n/a	chr7:100253746-100253755
6	REST	chr7:100253271-100254359	PFSK-1	brain:	n/a	chr7:100254148-100254161 chr7:100253640-100253654 chr7:100253625-100253638
7	REST	chr7:100253116-100254549	K562	blood:	n/a	chr7:100254148-100254161 chr7:100253640-100253654 chr7:100253625-100253638

No.	Distal block	Cell Line	Cell type
1	chr7:100237538..100239749-chr7:100251463..100254292,3	K562	blood:
2	chr7:100182086..100185168-chr7:100253147..100256450,3	MCF-7	breast:
3	chr7:100253224..100257564-chr7:100270253..100273768,4	K562	blood:
4	chr7:100243068..100245552-chr7:100251796..100254124,2	K562	blood:

Variant related genes	Relation type
ACTL6B	TF binding region
ENSG00000106336	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000077080	Chromatin interaction
ENSG00000077454	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10487157	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10953301	0.81[CHB][hapmap]
rs11520986	0.81[CHB][hapmap]
rs11764045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11770534	0.87[ASN][1000 genomes]
rs11772667	0.91[ASN][1000 genomes]
rs11974395	0.81[CHB][hapmap]
rs12532878	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2075672	0.86[JPT][hapmap]
rs2075674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2231172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2272572	0.81[CHB][hapmap]
rs4727459	0.81[CHB][hapmap]
rs4729597	0.86[JPT][hapmap]
rs4729601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4729602	0.81[CHB][hapmap]
rs62482242	0.82[ASN][1000 genomes]
rs6969584	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6969697	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs73156234	0.82[ASN][1000 genomes]
rs73170760	0.93[ASN][1000 genomes]
rs7385804	0.86[JPT][hapmap]
rs7786877	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7812123	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7812235	0.89[CHB][hapmap];1.00[JPT][hapmap]

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	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv607934	chr7:100240505-100271521	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100252600-100253400	Enhancers	Fetal Brain Male	brain
2	chr7:100252600-100253400	Enhancers	Gastric	stomach
3	chr7:100252600-100253600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:100252600-100254400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr7:100252800-100253400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:100252800-100253600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
7	chr7:100252800-100253600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:100252800-100254000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:100253000-100253400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr7:100253000-100253400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr7:100253000-100253600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr7:100253000-100253600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr7:100253000-100253600	Flanking Active TSS	Fetal Brain Female	brain
14	chr7:100253000-100254200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr7:100253000-100254200	ZNF genes & repeats	Spleen	Spleen
16	chr7:100253200-100253400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:100253200-100253600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr7:100253200-100254200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr7:100253200-100254400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr7:100253200-100254600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
21	chr7:100253200-100254600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links