Variant report

Variant	rs932447
Chromosome Location	chr1:57170229-57170230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:55923553..55925423-chr1:57168281..57171195,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10749708	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789036	0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs10789038	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789040	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789041	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889006	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10889008	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10889009	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206884	0.88[ASN][1000 genomes]
rs11206885	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206886	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11206888	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206889	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206890	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11206895	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1124900	0.81[CEU][hapmap]
rs11589368	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804779	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12021768	0.88[ASN][1000 genomes]
rs12021851	0.88[ASN][1000 genomes]
rs12023668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032999	0.86[ASN][1000 genomes]
rs12048572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073311	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12078260	0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[ASN][1000 genomes]
rs12092267	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097148	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12738355	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374924	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986660	0.88[ASN][1000 genomes]
rs2092595	0.81[CEU][hapmap]
rs2143754	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs2245475	0.81[AMR][1000 genomes]
rs2404718	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2404992	0.88[ASN][1000 genomes]
rs2404993	0.88[ASN][1000 genomes]
rs2746338	0.81[CEU][hapmap]
rs2746339	0.81[CEU][hapmap]
rs2746345	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2746348	0.81[CEU][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs2746349	0.81[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs2746353	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796495	0.81[CEU][hapmap]
rs2796498	0.81[CEU][hapmap]
rs2796509	0.85[CEU][hapmap]
rs2796512	0.84[CEU][hapmap]
rs2796517	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796519	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796523	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796527	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796534	0.83[CEU][hapmap]
rs4548471	0.88[ASN][1000 genomes]
rs4551620	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4562656	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4584419	0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs59223968	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61772962	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61774287	0.88[ASN][1000 genomes]
rs6588641	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6683935	0.81[AMR][1000 genomes]
rs715405	0.81[CEU][hapmap]
rs72666470	0.83[ASN][1000 genomes]
rs7415042	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs7419053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519509	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[ASN][1000 genomes]
rs7533440	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546264	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547486	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs857147	0.81[CEU][hapmap]
rs857148	0.81[CEU][hapmap]
rs857155	0.85[CEU][hapmap]
rs9887834	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887940	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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
rs932447	C1orf175	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:57154200-57174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:57154400-57174600	Weak transcription	Brain Anterior Caudate	brain
5	chr1:57154400-57174800	Weak transcription	Gastric	stomach
6	chr1:57159600-57172800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:57159800-57174800	Weak transcription	Fetal Stomach	stomach
8	chr1:57160000-57174800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:57160200-57174600	Weak transcription	Fetal Brain Male	brain
10	chr1:57160400-57174800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:57162600-57174600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:57162800-57176200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:57166200-57174800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:57166200-57178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:57166400-57171800	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:57166600-57171800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:57166600-57175600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:57166600-57175600	Weak transcription	Right Ventricle	heart
19	chr1:57169000-57174400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:57169200-57170400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:57169200-57170600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr1:57169600-57170400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:57169800-57172400	Strong transcription	HepG2	liver
24	chr1:57169800-57174800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:57170000-57170400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:57170000-57171800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:57170000-57173800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:57170000-57174200	Weak transcription	Psoas Muscle	Psoas
29	chr1:57170000-57174600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:57170000-57175200	Weak transcription	Fetal Intestine Large	intestine
31	chr1:57170000-57181200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:57170200-57170800	Weak transcription	Left Ventricle	heart
33	chr1:57170200-57171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:57170200-57171600	Weak transcription	Aorta	Aorta
35	chr1:57170200-57171600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:57170200-57171600	Weak transcription	A549	lung
37	chr1:57170200-57171600	Weak transcription	Hela-S3	cervix
38	chr1:57170200-57171800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:57170200-57171800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:57170200-57171800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:57170200-57172600	Weak transcription	Fetal Brain Female	brain
42	chr1:57170200-57172800	Weak transcription	Fetal Kidney	kidney
43	chr1:57170200-57173400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:57170200-57173600	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:57170200-57174800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:57170200-57174800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:57170200-57174800	Weak transcription	Pancreas	Pancrea
48	chr1:57170200-57175200	Weak transcription	Fetal Heart	heart
49	chr1:57170200-57175200	Weak transcription	Ovary	ovary
50	chr1:57170200-57175800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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