Variant report

Variant	rs3810831
Chromosome Location	chr2:87018547-87018548
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	MAX	chr2:87018445-87019083	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr2:87018349-87018915	K562	blood:	n/a	chr2:87018627-87018635
3	E2F6	chr2:87018324-87019221	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr2:87018081-87018551	GM12878	blood:	n/a	n/a
5	SMC3	chr2:87018521-87018767	Hela-S3	cervix:	n/a	n/a
6	SIN3A	chr2:87017074-87019173	H1-hESC	embryonic stem cell:	n/a	chr2:87019052-87019065 chr2:87018853-87018864
7	STAT1	chr2:87018355-87018575	GM12878	blood:	n/a	chr2:87018517-87018529
8	USF2	chr2:87018381-87018701	GM12878	blood:	n/a	chr2:87018544-87018560
9	CHD2	chr2:87018246-87019090	H1-hESC	embryonic stem cell:	n/a	n/a
10	SUZ12	chr2:87015893-87019035	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr2:87017499-87019101	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr2:87018294-87018729	GM12878	blood:	n/a	chr2:87018659-87018673 chr2:87018438-87018452
13	EP300	chr2:87018077-87018922	HepG2	liver:	n/a	chr2:87018659-87018673 chr2:87018438-87018452
14	CHD2	chr2:87018146-87018931	GM12878	blood:	n/a	n/a
15	MXI1	chr2:87018033-87018549	GM12878	blood:	n/a	n/a
16	JUND	chr2:87017924-87018942	H1-hESC	embryonic stem cell:	n/a	chr2:87018081-87018090 chr2:87018627-87018635
17	MAX	chr2:87018452-87019072	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CD8A	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11547281	0.86[CHB][hapmap]
rs12612585	0.82[CHD][hapmap]
rs12994456	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004867	1.00[JPT][hapmap]
rs13019439	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023213	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024420	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs13024609	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032379	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515950	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2944250	0.89[EUR][1000 genomes]
rs2944254	1.00[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3020726	1.00[ASN][1000 genomes]
rs3020728	0.87[ASN][1000 genomes]
rs34198915	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34256565	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34492196	1.00[ASN][1000 genomes]
rs34546581	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34613828	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34813683	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34855635	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34988194	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35290870	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35437846	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35505884	0.97[ASN][1000 genomes]
rs35626322	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35723887	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35739120	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35786939	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4366909	1.00[ASN][1000 genomes]
rs4605372	1.00[JPT][hapmap]
rs4832315	0.85[ASN][1000 genomes]
rs55816457	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55817008	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710361	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755452	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411867	1.00[ASN][1000 genomes]
rs71411868	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71411869	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7569868	0.83[AFR][1000 genomes]
rs7596329	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3810831	POLR1A	cis	cerebellum	SCAN
rs3810831	VPS24	cis	parietal	SCAN
rs3810831	RETSAT	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:87015600-87018800	Bivalent Enhancer	Fetal Brain Male	brain
2	chr2:87016000-87018600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:87016000-87018600	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
4	chr2:87016000-87019000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
5	chr2:87016200-87018600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr2:87016200-87018600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:87016200-87018600	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr2:87016800-87019000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr2:87017200-87018600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:87017200-87018800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:87017200-87018800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:87017200-87019000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:87017200-87019000	Bivalent Enhancer	Lung	lung
14	chr2:87017400-87018600	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:87017400-87019000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr2:87017400-87019000	Bivalent Enhancer	Placenta	Placenta
17	chr2:87017400-87019200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:87017600-87018800	Bivalent Enhancer	Liver	Liver
19	chr2:87017600-87019000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:87017600-87019000	Flanking Active TSS	Spleen	Spleen
21	chr2:87017600-87019600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr2:87017600-87020400	Active TSS	Thymus	Thymus
23	chr2:87017800-87018600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr2:87017800-87018600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:87017800-87019000	Enhancers	Pancreas	Pancrea
26	chr2:87017800-87019000	Bivalent Enhancer	GM12878-XiMat	blood
27	chr2:87018000-87018600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
29	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr2:87018000-87018600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
36	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
37	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
39	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
42	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
48	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
49	chr2:87018000-87018800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr2:87018000-87019000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood

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