Variant report

Variant	rs596784
Chromosome Location	chr1:57744259-57744260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs127600	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1424473	0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1811700	0.84[ASW][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap]
rs197635	0.90[ASN][1000 genomes]
rs197636	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs197637	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs197639	0.89[ASN][1000 genomes]
rs197640	0.89[ASN][1000 genomes]
rs197641	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs197642	1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2764664	0.96[CEU][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2764665	0.86[MEX][hapmap]
rs2764666	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs492781	0.95[MEX][hapmap];0.93[TSI][hapmap]
rs499397	0.81[MEX][hapmap]
rs511707	0.90[MEX][hapmap];0.82[TSI][hapmap]
rs514350	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs545582	0.90[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs552727	0.89[ASN][1000 genomes]
rs561531	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565846	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs581886	0.87[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes]
rs584147	0.86[MEX][hapmap]
rs595513	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs597941	0.83[TSI][hapmap]
rs606497	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs622423	0.93[LWK][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes]
rs626212	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs627550	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs643382	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs648607	0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs657471	0.90[CHD][hapmap];0.87[JPT][hapmap]
rs663975	0.81[MEX][hapmap];0.83[TSI][hapmap]
rs674966	0.96[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs706379	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs706385	0.90[MEX][hapmap];0.83[TSI][hapmap]
rs7529737	0.92[YRI][hapmap]
rs833626	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs596784	C1orf175	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57735200-57747200	Weak transcription	Esophagus	oesophagus
2	chr1:57737400-57746800	Weak transcription	Fetal Brain Female	brain
3	chr1:57741800-57749400	Enhancers	Fetal Intestine Small	intestine
4	chr1:57742000-57749200	Enhancers	Liver	Liver
5	chr1:57742200-57755400	Weak transcription	Fetal Brain Male	brain
6	chr1:57743000-57744400	Genic enhancers	Fetal Intestine Large	intestine
7	chr1:57743200-57745600	Enhancers	NHEK	skin
8	chr1:57743400-57745400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:57743800-57745000	Weak transcription	HMEC	breast
10	chr1:57743800-57745200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:57743800-57745200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:57743800-57745400	Enhancers	HepG2	liver
13	chr1:57744000-57745200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:57744200-57744600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:57744200-57744600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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