Variant report

Variant	rs4900969
Chromosome Location	chr14:38023289-38023290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:38021477..38023434-chr14:38051873..38053665,2	MCF-7	breast:
2	chr14:38022489..38024339-chr14:38026702..38028833,2	MCF-7	breast:
3	chr14:38022120..38023729-chr14:38064020..38066950,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139865	Chromatin interaction
ENSG00000259087	Chromatin interaction
ENSG00000129514	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1008236	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1011818	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs10133391	0.89[EUR][1000 genomes]
rs10133438	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10143976	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10144334	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10145379	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs10145473	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]
rs10151200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10400689	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap]
rs1057536	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs11156961	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];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11156962	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs1154688	1.00[ASN][1000 genomes]
rs1155456	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1158700	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159151	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs11623989	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1169873	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs11846416	0.91[ASN][1000 genomes]
rs12147939	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12147950	0.84[GIH][hapmap];0.86[TSI][hapmap]
rs12437250	0.81[ASN][1000 genomes]
rs12879895	0.84[ASN][1000 genomes]
rs12881012	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12884204	0.86[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs12884884	0.88[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12893503	0.86[CHB][hapmap];0.92[CHD][hapmap];0.84[ASN][1000 genomes]
rs12894536	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12896270	0.81[ASN][1000 genomes]
rs12896336	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs12896760	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs1473715	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1474886	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs1547008	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1547009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17179078	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17768201	0.84[ASN][1000 genomes]
rs17768249	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs17768343	0.88[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1814005	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1884798	0.87[ASN][1000 genomes]
rs1884803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950520	0.81[ASN][1000 genomes]
rs1950824	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[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950826	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];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955934	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1955943	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs1956427	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1956433	1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1956434	0.81[ASN][1000 genomes]
rs1956435	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs1956436	0.81[ASN][1000 genomes]
rs1956437	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1956438	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956439	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956440	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1956442	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs1956443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1980675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1989084	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2006729	0.87[CHD][hapmap];0.82[ASN][1000 genomes]
rs2038438	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057274	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2146133	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2180609	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2415404	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs28397975	1.00[ASN][1000 genomes]
rs34982606	0.84[ASN][1000 genomes]
rs4898640	1.00[ASN][1000 genomes]
rs4900918	0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4900945	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4900958	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4900966	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900967	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4900971	1.00[ASN][1000 genomes]
rs4900972	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4901012	0.81[ASN][1000 genomes]
rs61988193	0.81[ASN][1000 genomes]
rs61988194	0.84[ASN][1000 genomes]
rs61988195	0.84[ASN][1000 genomes]
rs6571812	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs6571814	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs6571815	0.81[ASN][1000 genomes]
rs7143956	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144658	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs7145671	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs7145758	0.81[ASN][1000 genomes]
rs7146299	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7146593	0.81[ASN][1000 genomes]
rs7146958	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7147379	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs7148547	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7153426	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7153867	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7157247	0.81[ASN][1000 genomes]
rs7159456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7160774	0.81[ASN][1000 genomes]
rs7161228	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7161326	0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs7161366	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7493775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8005136	0.82[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs8008655	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs8016138	0.88[ASN][1000 genomes]
rs8019713	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs9322981	0.88[ASN][1000 genomes]
rs968350	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs996916	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[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	nsv564349	chr14:37890433-38034434	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4900969	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38014600-38035800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:38016200-38035800	Weak transcription	Stomach Mucosa	stomach
3	chr14:38023200-38023600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:38023200-38023600	Enhancers	Liver	Liver
5	chr14:38023200-38023800	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr14:38023200-38023800	Enhancers	HepG2	liver

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