Variant report

Variant	rs2092595
Chromosome Location	chr1:57145073-57145074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57131079..57133360-chr1:57142832..57145132,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10789038	0.89[CEU][hapmap]
rs10889008	0.85[CEU][hapmap]
rs10889010	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206889	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs11206890	0.85[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs11206899	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206900	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1124900	0.92[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12070903	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12072057	0.82[EUR][1000 genomes]
rs12738355	0.81[EUR][1000 genomes]
rs2064421	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064422	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2092594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143754	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245475	0.84[EUR][1000 genomes]
rs2746338	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2746339	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2746345	0.81[EUR][1000 genomes]
rs2746348	0.88[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs2746349	0.92[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs2796491	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2796492	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796493	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796495	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796496	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796498	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2796499	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796506	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2796507	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796509	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2796512	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796514	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2796517	0.81[EUR][1000 genomes]
rs2796519	0.85[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs2796523	0.81[EUR][1000 genomes]
rs2796527	0.81[EUR][1000 genomes]
rs2796534	0.84[CEU][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2796541	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6588643	0.85[EUR][1000 genomes]
rs6671760	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6683935	0.85[EUR][1000 genomes]
rs715404	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs715405	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7366969	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7367181	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7367199	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7415042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7419053	0.82[CEU][hapmap]
rs7515414	0.82[CEU][hapmap]
rs857132	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs857147	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs857148	0.92[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs857150	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs857155	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857156	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs857159	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs932447	0.81[CEU][hapmap]
rs963528	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	esv1831276	chr1:57139370-57175158	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	nsv520726	chr1:57143986-57205666	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2092595	C1orf175	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57122800-57169600	Weak transcription	Ovary	ovary
2	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
3	chr1:57129800-57152200	Weak transcription	Psoas Muscle	Psoas
4	chr1:57135400-57160200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:57136200-57161400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:57142600-57150400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:57143000-57153600	Weak transcription	NH-A	brain
8	chr1:57143400-57149400	Weak transcription	Fetal Heart	heart
9	chr1:57143600-57153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:57144000-57145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:57144000-57148800	Weak transcription	Hela-S3	cervix
12	chr1:57144000-57149200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
16	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:57145000-57146000	Strong transcription	Left Ventricle	heart
18	chr1:57145000-57146000	Strong transcription	HepG2	liver

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