Variant report

Variant	rs10190003
Chromosome Location	chr2:187357465-187357466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10169008	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10196955	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	1.00[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]
rs10200749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.89[ASN][1000 genomes]
rs11688988	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11692347	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11888880	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.89[ASN][1000 genomes]
rs11903027	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12328822	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13397188	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13428033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448848	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448849	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1448855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16827968	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1868383	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2084488	0.89[ASN][1000 genomes]
rs2084489	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2370688	0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.89[ASN][1000 genomes]
rs56137171	0.89[ASN][1000 genomes]
rs61434493	0.89[ASN][1000 genomes]
rs6434174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709401	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6710436	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717525	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6721789	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.89[ASN][1000 genomes]
rs6728400	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731567	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6744717	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7585905	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288129	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.89[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
rs10190003	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	chr2:187352000-187357800	Weak transcription	Pancreas	Pancrea
4	chr2:187352200-187365400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:187352200-187365400	Weak transcription	Lung	lung
6	chr2:187352400-187358000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:187352400-187358200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:187352400-187358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:187352400-187358400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:187352400-187358600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:187352400-187358800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:187352400-187358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:187352400-187358800	Enhancers	Colon Smooth Muscle	Colon
14	chr2:187352400-187358800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:187352400-187359000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:187352400-187359400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:187352400-187360000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:187352400-187360000	Weak transcription	Placenta	Placenta
19	chr2:187352600-187358000	Enhancers	Brain Angular Gyrus	brain
20	chr2:187352600-187358600	Enhancers	Brain Anterior Caudate	brain
21	chr2:187352600-187359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:187352600-187360200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:187352600-187360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:187352600-187360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:187352600-187362600	Weak transcription	HSMMtube	muscle
26	chr2:187353200-187357800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:187353200-187360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:187353400-187358200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:187353400-187360000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:187353400-187361800	Weak transcription	Fetal Heart	heart
31	chr2:187353600-187357600	Active TSS	GM12878-XiMat	blood
32	chr2:187353600-187357800	Weak transcription	Stomach Mucosa	stomach
33	chr2:187353600-187358000	Weak transcription	Right Atrium	heart
34	chr2:187353600-187358000	Weak transcription	Right Ventricle	heart
35	chr2:187353600-187358000	Weak transcription	HSMM	muscle
36	chr2:187353600-187359800	Weak transcription	Osteobl	bone
37	chr2:187353600-187361200	Weak transcription	Fetal Brain Male	brain
38	chr2:187353600-187362600	Weak transcription	Fetal Stomach	stomach
39	chr2:187353800-187357800	Enhancers	Primary T cells from cord blood	blood
40	chr2:187353800-187358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:187353800-187358800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr2:187353800-187358800	Genic enhancers	HepG2	liver
43	chr2:187353800-187359400	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:187353800-187359800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:187353800-187360000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:187353800-187360000	Weak transcription	Colonic Mucosa	Colon
47	chr2:187353800-187360200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:187353800-187360800	Weak transcription	Brain Germinal Matrix	brain
49	chr2:187353800-187361000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:187353800-187361000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links