Variant report

Variant	rs2197139
Chromosome Location	chr2:187358367-187358368
allele	A/C/G/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	POLR2A	chr2:187357577-187358906	K562	blood:	n/a	n/a
2	POLR2A	chr2:187358257-187358796	K562	blood:	n/a	n/a
3	POLR2A	chr2:187358194-187358802	K562	blood:	n/a	n/a
4	POLR2A	chr2:187358237-187358800	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:187358195-187358822	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:187358045-187358912	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187356824..187359065-chr20:55840878..55843076,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213953	TF binding region
DPRXP1	TF binding region
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10177153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178888	0.85[EUR][1000 genomes]
rs10181681	0.80[EUR][1000 genomes]
rs10190003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10196955	0.89[ASN][1000 genomes]
rs10198525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10200749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10208643	0.89[ASN][1000 genomes]
rs1037241	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10497672	0.83[CEU][hapmap]
rs11675633	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675656	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11678950	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11680486	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688988	0.89[ASN][1000 genomes]
rs11690758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692028	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692347	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693797	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11888432	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11895483	0.82[EUR][1000 genomes]
rs11898666	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901465	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328822	0.89[ASN][1000 genomes]
rs13392819	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393891	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13394241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13397188	0.89[ASN][1000 genomes]
rs13401304	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13428033	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448848	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827968	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827994	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1868383	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869031	0.83[EUR][1000 genomes]
rs2044683	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084488	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084489	0.89[ASN][1000 genomes]
rs2084490	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370688	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887826	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642346	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719959	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56137171	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61226319	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61434493	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434167	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709401	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6716324	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717525	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721789	0.89[ASN][1000 genomes]
rs6724161	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728382	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731567	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6744717	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72893450	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72895449	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72897386	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72901315	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72901322	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7579259	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584137	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585889	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588607	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597954	0.89[ASN][1000 genomes]
rs7603088	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288129	0.89[ASN][1000 genomes]
rs9917285	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2197139	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187351800-187361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:187351800-187362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:187352200-187365400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:187352200-187365400	Weak transcription	Lung	lung
5	chr2:187352400-187358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:187352400-187358400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:187352400-187358600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:187352400-187358800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:187352400-187358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:187352400-187358800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:187352400-187358800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr2:187352400-187359000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:187352400-187359400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:187352400-187360000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:187352400-187360000	Weak transcription	Placenta	Placenta
16	chr2:187352600-187358600	Enhancers	Brain Anterior Caudate	brain
17	chr2:187352600-187359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:187352600-187360200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:187352600-187360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:187352600-187360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:187352600-187362600	Weak transcription	HSMMtube	muscle
22	chr2:187353200-187360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:187353400-187360000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:187353400-187361800	Weak transcription	Fetal Heart	heart
25	chr2:187353600-187359800	Weak transcription	Osteobl	bone
26	chr2:187353600-187361200	Weak transcription	Fetal Brain Male	brain
27	chr2:187353600-187362600	Weak transcription	Fetal Stomach	stomach
28	chr2:187353800-187358800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:187353800-187358800	Genic enhancers	HepG2	liver
30	chr2:187353800-187359400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:187353800-187359800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:187353800-187360000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:187353800-187360000	Weak transcription	Colonic Mucosa	Colon
34	chr2:187353800-187360200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:187353800-187360800	Weak transcription	Brain Germinal Matrix	brain
36	chr2:187353800-187361000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:187353800-187361000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:187353800-187362600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:187354000-187359800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:187354000-187360000	Weak transcription	NHLF	lung
41	chr2:187354000-187360200	Weak transcription	Fetal Kidney	kidney
42	chr2:187354000-187360200	Weak transcription	Fetal Lung	lung
43	chr2:187354000-187360200	Weak transcription	NH-A	brain
44	chr2:187354000-187365200	Weak transcription	Thymus	Thymus
45	chr2:187354200-187360000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:187354400-187360200	Weak transcription	Fetal Intestine Large	intestine
47	chr2:187354600-187358600	Genic enhancers	K562	blood
48	chr2:187354600-187360000	Weak transcription	NHDF-Ad	bronchial
49	chr2:187354600-187360200	Weak transcription	Primary B cells from cord blood	blood
50	chr2:187354600-187360800	Weak transcription	Primary hematopoietic stem cells	blood

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