Variant report

Variant	rs4385188
Chromosome Location	chr5:74734362-74734363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74728841..74731298-chr5:74732916..74734821,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10038723	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10043621	0.84[ASN][1000 genomes]
rs10044053	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10053643	0.82[ASN][1000 genomes]
rs10060260	0.81[EUR][1000 genomes]
rs10067641	0.83[EUR][1000 genomes]
rs10070207	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10075139	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10434644	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10462517	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10473972	0.82[ASN][1000 genomes]
rs10474433	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs10474434	0.82[ASN][1000 genomes]
rs10474436	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051795	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10942739	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11957913	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12234032	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13354407	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1427924	0.83[EUR][1000 genomes]
rs17238484	0.82[ASN][1000 genomes]
rs17739580	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1863934	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1863935	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995267	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287711	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs253392	0.83[JPT][hapmap]
rs253393	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs253407	0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs253409	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs28609217	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2878519	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2878520	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3213801	0.80[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3761742	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3761743	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846665	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846666	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3931914	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4045166	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4440336	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703670	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4703674	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4704214	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4704224	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57149337	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57312935	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5744533	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744555	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744575	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5744595	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744598	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs5744601	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5744621	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744663	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744703	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59506842	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61430233	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6453134	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67969809	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6861279	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6863398	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6872314	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874781	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6886841	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6891949	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698912	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73120833	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7356637	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7445415	0.85[ASN][1000 genomes]
rs767676	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7700468	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701925	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7706857	0.83[EUR][1000 genomes]
rs7709282	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7717505	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7723531	0.83[EUR][1000 genomes]
rs7737959	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs924452	0.83[EUR][1000 genomes]
rs9293656	0.82[EUR][1000 genomes]
rs9332464	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs9885386	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882195	chr5:74678937-74896798	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised 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
4	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4385188	HMGCR	cis	cerebellum	SCAN
rs4385188	S100Z	cis	parietal	SCAN
rs4385188	COL4A3BP	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74674400-74761400	Weak transcription	Esophagus	oesophagus
2	chr5:74706200-74756400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:74708400-74746000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:74709600-74760200	Weak transcription	Gastric	stomach
5	chr5:74713200-74753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:74718800-74742200	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:74721400-74742600	Weak transcription	Thymus	Thymus
8	chr5:74721600-74736000	Weak transcription	Primary T cells from cord blood	blood
9	chr5:74721600-74741400	Weak transcription	Fetal Lung	lung
10	chr5:74721600-74742600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:74721800-74734400	Weak transcription	HMEC	breast
12	chr5:74721800-74741800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:74721800-74742600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:74721800-74749600	Weak transcription	Adipose Nuclei	Adipose
15	chr5:74722000-74737400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:74722200-74737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:74722200-74749800	Weak transcription	Liver	Liver
18	chr5:74722600-74738000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:74722600-74742200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:74722800-74735200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr5:74722800-74737400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:74723000-74741400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:74723200-74738000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:74725600-74741400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:74729800-74741400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:74730400-74757400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:74731200-74738400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr5:74731800-74737200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr5:74731800-74737400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:74731800-74741400	Weak transcription	Aorta	Aorta
31	chr5:74731800-74741600	Weak transcription	HSMMtube	muscle
32	chr5:74731800-74742400	Weak transcription	Ovary	ovary
33	chr5:74731800-74757400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:74732000-74742600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:74732000-74742600	Weak transcription	Lung	lung
36	chr5:74732000-74756800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:74732000-74760200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:74732000-74787400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:74732200-74735000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:74732200-74736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:74733000-74734800	Weak transcription	Primary B cells from cord blood	blood
42	chr5:74733000-74734800	Weak transcription	Fetal Stomach	stomach
43	chr5:74733000-74735400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:74733000-74737400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:74734200-74735400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:74734200-74735400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr5:74734200-74735400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr5:74734200-74735600	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links