Variant report

Variant	rs7419053
Chromosome Location	chr1:57158293-57158294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10749708	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789036	0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10789038	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10789040	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10789041	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889006	0.84[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];0.90[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10889009	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10889010	0.81[EUR][1000 genomes]
rs11206884	0.88[ASN][1000 genomes]
rs11206885	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11206886	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11206888	0.84[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];0.90[MEX][hapmap];0.84[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];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11206895	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1124900	0.82[CEU][hapmap]
rs11589368	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804779	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12021768	0.88[ASN][1000 genomes]
rs12021851	0.88[ASN][1000 genomes]
rs12023668	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032999	0.86[ASN][1000 genomes]
rs12048572	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073311	0.84[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	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097148	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12738355	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13374924	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418442	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986660	0.88[ASN][1000 genomes]
rs2092595	0.82[CEU][hapmap]
rs2143754	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs2404718	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2404992	0.88[ASN][1000 genomes]
rs2404993	0.88[ASN][1000 genomes]
rs2746338	0.82[CEU][hapmap]
rs2746339	0.82[CEU][hapmap]
rs2746345	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2746348	0.85[MEX][hapmap]
rs2746349	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs2746353	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2796495	0.82[CEU][hapmap]
rs2796498	0.82[CEU][hapmap]
rs2796509	0.85[CEU][hapmap]
rs2796512	0.85[CEU][hapmap]
rs2796517	0.89[AMR][1000 genomes];0.83[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];0.90[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796523	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2796527	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4548471	0.88[ASN][1000 genomes]
rs4551620	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4562656	0.80[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];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs59223968	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61772962	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61774287	0.88[ASN][1000 genomes]
rs6588641	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs715405	0.82[CEU][hapmap]
rs72666470	0.83[ASN][1000 genomes]
rs7415042	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7515414	1.00[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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[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];0.86[MEX][hapmap];0.85[ASN][1000 genomes]
rs7533440	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546264	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547486	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs857147	0.82[CEU][hapmap]
rs857148	0.82[CEU][hapmap]
rs857155	0.85[CEU][hapmap]
rs932447	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]
rs9887834	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887940	0.88[AMR][1000 genomes];0.93[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
rs7419053	C1orf175	cis	parietal	SCAN

Chromatin state (count:30 , 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	chr1:57135400-57160200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:57136200-57161400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:57144200-57165000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:57144200-57171800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:57144400-57169400	Weak transcription	Fetal Kidney	kidney
8	chr1:57144400-57173600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:57149600-57166000	Weak transcription	Right Ventricle	heart
10	chr1:57150000-57165800	Weak transcription	Left Ventricle	heart
11	chr1:57150600-57168000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:57151000-57165600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:57151400-57165400	Weak transcription	Fetal Heart	heart
14	chr1:57152400-57165800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:57154200-57174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:57154400-57166000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:57154400-57169000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:57154400-57174600	Weak transcription	Brain Anterior Caudate	brain
19	chr1:57154400-57174800	Weak transcription	Gastric	stomach
20	chr1:57154600-57160000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:57154600-57165200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:57154600-57169800	Weak transcription	Fetal Intestine Large	intestine
23	chr1:57154800-57161200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:57154800-57162000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:57154800-57165800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:57154800-57166000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:57155000-57161400	Weak transcription	HepG2	liver
28	chr1:57155000-57162200	Weak transcription	A549	lung
29	chr1:57156600-57165800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:57157400-57158400	Strong transcription	Hela-S3	cervix

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