Variant report

Variant	rs7415042
Chromosome Location	chr1:57151954-57151955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10789038	0.92[CEU][hapmap]
rs10789040	0.81[EUR][1000 genomes]
rs10789041	0.80[EUR][1000 genomes]
rs10889008	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10889009	0.81[EUR][1000 genomes]
rs10889010	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206889	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs11206890	0.89[CEU][hapmap]
rs11206899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206900	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1124900	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs11589368	0.82[EUR][1000 genomes]
rs11804779	0.82[EUR][1000 genomes]
rs12070903	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12092267	0.81[EUR][1000 genomes]
rs12097148	0.81[EUR][1000 genomes]
rs13374924	0.82[EUR][1000 genomes]
rs1418442	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2064421	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2064422	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2092594	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092595	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]
rs2143754	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2746338	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2746339	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2746348	0.92[CEU][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs2746349	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs2796491	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796492	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796493	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796495	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796496	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796498	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796499	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796506	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2796507	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796511	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2796512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796514	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2796519	0.89[CEU][hapmap]
rs2796534	0.88[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2796541	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6671760	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs715404	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs715405	0.96[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7366969	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7367181	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7367199	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7419053	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7515414	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7533440	0.81[EUR][1000 genomes]
rs7545066	0.81[EUR][1000 genomes]
rs857132	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs857147	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs857148	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs857150	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs857155	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs857156	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs857159	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs932447	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs963528	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9887834	0.81[EUR][1000 genomes]
rs9887940	0.81[EUR][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
rs7415042	C1orf175	cis	parietal	SCAN

Chromatin state (count:25 , 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	chr1:57143000-57153600	Weak transcription	NH-A	brain
7	chr1:57143600-57153600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
11	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:57148800-57152600	Enhancers	Hela-S3	cervix
13	chr1:57149600-57166000	Weak transcription	Right Ventricle	heart
14	chr1:57150000-57165800	Weak transcription	Left Ventricle	heart
15	chr1:57150600-57152000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:57150600-57152000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:57150600-57168000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:57151000-57165600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:57151400-57152200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:57151400-57153600	Enhancers	A549	lung
21	chr1:57151400-57165400	Weak transcription	Fetal Heart	heart
22	chr1:57151800-57152400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:57151800-57152400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:57151800-57152600	Enhancers	HepG2	liver
25	chr1:57151800-57152800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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