Variant report

Variant	rs4075325
Chromosome Location	chr12:57649840-57649841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57649270..57651389-chr12:57651835..57654248,2	MCF-7	breast:
2	chr12:57649151..57651575-chr12:57664952..57666883,3	K562	blood:
3	chr12:57642653..57645181-chr12:57648968..57650565,2	K562	blood:
4	chr12:57636983..57640050-chr12:57648004..57652445,5	K562	blood:

Variant related genes	Relation type
ENSG00000185482	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783818	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10783819	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783820	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783823	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10876976	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs10876978	0.80[AMR][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs11172160	0.88[EUR][1000 genomes]
rs11172165	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11172169	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs11172170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11172190	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11609986	0.93[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12296766	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12310220	0.80[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12579911	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.96[CEU][hapmap];0.85[CHB][hapmap]
rs1798710	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs2063778	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs3923885	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4760192	0.86[EUR][1000 genomes]
rs4760193	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4760228	0.82[AMR][1000 genomes]
rs4760236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4760348	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760356	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760357	0.82[AMR][1000 genomes]
rs481196	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs491750	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs512223	0.82[AMR][1000 genomes]
rs533975	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs537482	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs543410	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap]
rs560048	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs568793	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs575153	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs6581131	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581134	0.87[ASW][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581135	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581136	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6581139	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7132367	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7133366	0.83[AMR][1000 genomes]
rs7133939	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7135142	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7298418	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7307059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7309659	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7313824	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7314266	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7358684	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7398058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7486863	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7977908	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4075325	OR6C4	cis	parietal	SCAN
rs4075325	ZNF385A	cis	parietal	SCAN
rs4075325	SILV	cis	parietal	SCAN
rs4075325	TSPAN31	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57637600-57651200	Weak transcription	NHDF-Ad	bronchial
2	chr12:57637600-57654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57638000-57651200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57638000-57651200	Weak transcription	Fetal Brain Male	brain
5	chr12:57638800-57673600	Weak transcription	Stomach Mucosa	stomach
6	chr12:57639600-57651200	Weak transcription	Hela-S3	cervix
7	chr12:57639600-57651200	Weak transcription	HepG2	liver
8	chr12:57642800-57651000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:57643800-57651000	Weak transcription	K562	blood
10	chr12:57645000-57650000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:57645000-57651400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:57645000-57651600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:57645000-57651600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:57645000-57652400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:57645200-57650000	Weak transcription	HSMMtube	muscle
16	chr12:57645200-57651600	Weak transcription	Psoas Muscle	Psoas
17	chr12:57645200-57655600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:57646000-57667600	Strong transcription	Thymus	Thymus
19	chr12:57646200-57657000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:57646800-57651000	Weak transcription	HUVEC	blood vessel
21	chr12:57647000-57650400	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr12:57647000-57653000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:57647000-57655800	Strong transcription	Fetal Intestine Small	intestine
24	chr12:57647000-57657000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:57647000-57657200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr12:57647200-57652600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:57647200-57654600	Strong transcription	Fetal Brain Female	brain
28	chr12:57647200-57655200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:57647200-57655600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:57647200-57656600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr12:57647200-57657000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr12:57647200-57657200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:57647200-57657200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:57647200-57657400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:57647200-57657800	Strong transcription	Fetal Thymus	thymus
36	chr12:57647200-57668200	Strong transcription	Fetal Stomach	stomach
37	chr12:57647400-57651800	Weak transcription	HMEC	breast
38	chr12:57647400-57654400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:57648000-57653800	Weak transcription	Right Atrium	heart
40	chr12:57648000-57657200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:57648000-57657200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:57648000-57657400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:57648000-57657400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:57648200-57650200	Weak transcription	NH-A	brain
45	chr12:57648200-57653800	Strong transcription	Brain Germinal Matrix	brain
46	chr12:57648200-57654400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:57648200-57655800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:57648200-57657400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:57648200-57657400	Strong transcription	Primary T cells from cord blood	blood
50	chr12:57648400-57650200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links