Variant report

Variant	rs10145473
Chromosome Location	chr14:38035841-38035842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:38035709..38036660-chr14:38064999..38065756,3	MCF-7	breast:
2	chr14:38035794..38036299-chr14:38056945..38057588,2	MCF-7	breast:
3	chr14:38035462..38036377-chr14:38063741..38064636,2	MCF-7	breast:
4	chr14:38035774..38036456-chr14:38064681..38065639,3	MCF-7	breast:
5	chr14:38035549..38036658-chr14:38063068..38063787,3	MCF-7	breast:
6	chr14:38035593..38036192-chr14:38052628..38053371,2	MCF-7	breast:
7	chr14:38035755..38036301-chr14:38065026..38065953,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129514	Chromatin interaction
ENSG00000139865	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1008236	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs1011818	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10133391	0.81[EUR][1000 genomes]
rs10133438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10143976	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs10144334	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145379	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10151200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10400689	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs1057536	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs11156961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11156962	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1154688	0.91[ASN][1000 genomes]
rs1155456	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1158700	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1158701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1159151	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11623989	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs11627807	0.82[ASN][1000 genomes]
rs1169873	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs11846416	1.00[ASN][1000 genomes]
rs12147939	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12147950	0.82[GIH][hapmap];0.88[TSI][hapmap]
rs12881012	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12884204	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs12884884	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs12893503	0.86[CHB][hapmap];0.96[CHD][hapmap]
rs12894536	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs12896336	0.86[CHB][hapmap]
rs12896760	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1473715	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1474886	0.86[CHB][hapmap]
rs1547008	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1547009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17179078	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs17768249	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs17768343	0.88[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap]
rs1814005	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1884798	0.96[ASN][1000 genomes]
rs1884803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1950824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1950826	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955934	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1955943	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1956427	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1956429	0.82[ASN][1000 genomes]
rs1956433	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1956435	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1956437	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1956438	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1956439	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1956440	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1956442	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs1956443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1980675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989084	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2006729	0.91[CHD][hapmap]
rs2038438	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2057274	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2146133	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs2180609	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs2415404	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs28397975	0.91[ASN][1000 genomes]
rs4898640	0.91[ASN][1000 genomes]
rs4900918	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs4900945	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4900958	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4900966	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900967	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4900971	0.91[ASN][1000 genomes]
rs4900972	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4901012	0.90[ASN][1000 genomes]
rs6571812	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs6571814	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7143956	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144658	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs7145671	0.85[CHB][hapmap];0.96[CHD][hapmap]
rs7146299	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7146958	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147379	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs7148547	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7153426	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7153867	1.00[ASN][1000 genomes]
rs7159456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7160774	0.90[ASN][1000 genomes]
rs7161228	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7161326	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs7161366	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7493775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762083	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8005136	0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs8008655	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs8016138	0.97[ASN][1000 genomes]
rs8019713	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs9322981	0.97[ASN][1000 genomes]
rs968350	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs996916	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv901639	chr14:37743583-38038468	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv901641	chr14:37939401-38040755	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv826923	chr14:38017619-38108645	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv832772	chr14:38030300-38225921	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10145473	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38034600-38036200	Active TSS	Colonic Mucosa	Colon
2	chr14:38035000-38036000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr14:38035200-38036400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr14:38035400-38036800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr14:38035400-38037200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr14:38035600-38037200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:38035600-38037400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr14:38035800-38036000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr14:38035800-38036200	Active TSS	Rectal Smooth Muscle	rectum
10	chr14:38035800-38036200	Enhancers	Stomach Mucosa	stomach
11	chr14:38035800-38036400	Enhancers	H9 Cell Line	embryonic stem cell
12	chr14:38035800-38036400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr14:38035800-38036400	Enhancers	Aorta	Aorta
14	chr14:38035800-38036400	Flanking Active TSS	A549	lung
15	chr14:38035800-38036600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr14:38035800-38036600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr14:38035800-38036600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:38035800-38036600	Flanking Active TSS	Liver	Liver
19	chr14:38035800-38037200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr14:38035800-38037200	Enhancers	HepG2	liver
21	chr14:38035800-38037400	Enhancers	Hela-S3	cervix
22	chr14:38035800-38037400	Enhancers	HUVEC	blood vessel

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