Variant report

Variant	rs1955943
Chromosome Location	chr14:37925120-37925121
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:37923826..37925404-chr14:38041177..38044020,2	MCF-7	breast:
2	chr14:37923519..37926055-chr14:37998366..38001362,2	MCF-7	breast:
3	chr14:37924566..37927073-chr14:38060566..38062784,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1011818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10132119	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs10133438	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10134502	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs10137741	0.84[AMR][1000 genomes]
rs10139938	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs10141058	0.83[GIH][hapmap];0.85[TSI][hapmap]
rs10143976	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10145379	0.83[CHD][hapmap]
rs10145473	0.86[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs10145536	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs10146056	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs10150919	0.83[GIH][hapmap]
rs10151106	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs10151200	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10400689	0.83[CHD][hapmap]
rs1057536	0.83[CHD][hapmap]
rs11156943	0.85[GIH][hapmap];0.84[TSI][hapmap]
rs11156961	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11156962	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs1155456	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11560071	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1158701	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1159151	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11623989	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1169871	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1169872	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1169873	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1169875	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12147939	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12437250	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12879895	0.85[AMR][1000 genomes]
rs12881012	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12884204	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs12886692	0.83[GIH][hapmap];0.85[TSI][hapmap]
rs12893226	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12893503	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs12894536	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896270	0.85[AMR][1000 genomes]
rs12896336	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs12896760	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1474886	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs1546975	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs1547008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1547009	0.87[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs17106539	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs17179057	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17179078	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768201	0.85[AMR][1000 genomes]
rs17768249	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768254	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814005	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1884803	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs1950520	0.81[AMR][1000 genomes]
rs1950526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.92[TSI][hapmap]
rs1950824	0.86[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs1950826	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs1955934	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1955938	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs1955939	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs1955949	1.00[ASW][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955950	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs1956427	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1956433	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956434	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1956435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1956436	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1956437	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1956442	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1956443	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1980675	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1989084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2006062	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2006729	1.00[ASW][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2064669	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs2103890	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs2146133	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2180609	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2208211	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415404	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34609612	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34718937	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34781514	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34955525	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34982606	0.85[AMR][1000 genomes]
rs35005938	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35137324	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35310650	0.98[ASN][1000 genomes]
rs3985275	0.85[GIH][hapmap];0.87[TSI][hapmap]
rs4444242	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4900820	0.81[TSI][hapmap]
rs4900918	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4900945	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs4900969	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs61988193	0.84[AMR][1000 genomes]
rs61988194	0.85[AMR][1000 genomes]
rs61988195	0.85[AMR][1000 genomes]
rs6571812	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571814	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6571815	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145592	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145671	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145758	0.92[ASN][1000 genomes]
rs7146299	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7146593	0.85[AMR][1000 genomes]
rs7147101	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7151222	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs7153426	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7157247	0.85[AMR][1000 genomes]
rs7159004	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7159456	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs7161326	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7161366	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7492724	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7493775	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs8005136	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs8008655	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996916	0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs9989229	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv915783	chr14:37607836-38002966	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036854	chr14:37609535-38013533	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv542045	chr14:37609535-38013533	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	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
6	nsv901640	chr14:37782273-37963104	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949227	chr14:37785560-37963104	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1851939	chr14:37810699-37963104	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv530639	chr14:37837079-37934746	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1043093	chr14:37849742-37928753	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1955943	FOXA1	cis	parietal	SCAN
rs1955943	TRAPPC6B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:37918400-37926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr14:37921400-37927800	Weak transcription	Esophagus	oesophagus
3	chr14:37922000-37926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:37922000-37926400	Weak transcription	HMEC	breast
5	chr14:37922200-37926400	Weak transcription	NHEK	skin
6	chr14:37922200-37950200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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