Variant report

Variant	rs2229032
Chromosome Location	chr3:142178144-142178145
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	POLR2A	chr3:142177863-142178323	K562	blood:	n/a	n/a
2	E2F4	chr3:142178017-142178217	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142165266..142167494-chr3:142176108..142178776,2	K562	blood:
2	chr3:142166774..142168881-chr3:142175818..142179023,4	MCF-7	breast:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10935464	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707154	0.84[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11708870	0.84[ASW][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11709758	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11711164	0.84[ASW][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11711179	0.93[ASN][1000 genomes]
rs11714244	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11714528	0.83[ASN][1000 genomes]
rs11719737	0.84[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11720007	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11720762	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17623058	0.81[CEU][hapmap]
rs2291363	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.80[ASN][1000 genomes]
rs2306700	0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28365824	0.85[EUR][1000 genomes]
rs3922731	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55687115	0.83[ASN][1000 genomes]
rs55994893	0.87[EUR][1000 genomes]
rs56088529	0.83[ASN][1000 genomes]
rs56397702	0.87[EUR][1000 genomes]
rs60001529	0.89[EUR][1000 genomes]
rs66597875	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769123	0.80[ASN][1000 genomes]
rs6778383	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs6780665	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs73228757	0.80[EUR][1000 genomes]
rs73228758	0.80[EUR][1000 genomes]
rs73238173	0.80[ASN][1000 genomes]
rs73238176	0.80[ASN][1000 genomes]
rs73238185	0.83[ASN][1000 genomes]
rs73238186	0.83[ASN][1000 genomes]
rs73238187	0.83[ASN][1000 genomes]
rs73238195	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238200	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73238201	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73238202	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73240305	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73240309	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73240310	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73240314	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73240316	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73240323	0.89[EUR][1000 genomes]
rs73240328	0.85[EUR][1000 genomes]
rs7633870	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7642634	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9858204	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142167200-142178800	Weak transcription	Small Intestine	intestine
2	chr3:142167200-142187600	Weak transcription	Esophagus	oesophagus
3	chr3:142167200-142192400	Weak transcription	Pancreas	Pancrea
4	chr3:142167400-142179600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:142167400-142199400	Weak transcription	Colonic Mucosa	Colon
6	chr3:142167400-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:142167400-142234600	Weak transcription	Psoas Muscle	Psoas
8	chr3:142167600-142180000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:142167600-142180000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:142167600-142187200	Weak transcription	Fetal Brain Male	brain
11	chr3:142167600-142191800	Weak transcription	Fetal Brain Female	brain
12	chr3:142167600-142199600	Weak transcription	Ovary	ovary
13	chr3:142167600-142200000	Weak transcription	HSMMtube	muscle
14	chr3:142167600-142203000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:142167800-142179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:142167800-142179800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:142167800-142180000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:142167800-142180200	Weak transcription	HepG2	liver
19	chr3:142167800-142184800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:142167800-142186400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:142167800-142188800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:142167800-142190400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:142167800-142199400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:142167800-142200000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:142167800-142200000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:142168000-142182600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:142168000-142192000	Weak transcription	Fetal Lung	lung
28	chr3:142168000-142200000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:142168000-142200000	Weak transcription	Fetal Kidney	kidney
30	chr3:142168200-142185800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:142168400-142180600	Strong transcription	Dnd41	blood
32	chr3:142168400-142186400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:142169000-142187000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:142169800-142192200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:142170200-142189200	Weak transcription	Aorta	Aorta
36	chr3:142170600-142199200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:142170600-142199600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:142170600-142203200	Weak transcription	Spleen	Spleen
39	chr3:142170800-142183200	Weak transcription	GM12878-XiMat	blood
40	chr3:142172400-142187600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:142172800-142199200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:142174000-142181400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:142174200-142180600	Strong transcription	A549	lung
44	chr3:142174400-142182600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:142174400-142184000	Weak transcription	Osteobl	bone
46	chr3:142174800-142178200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:142174800-142178800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:142174800-142179800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:142174800-142183600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:142174800-142186400	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links