Variant report

Variant	rs556204
Chromosome Location	chr1:57595583-57595584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11206975	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12090414	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12408256	1.00[JPT][hapmap]
rs12564278	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12566320	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17115105	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17115108	1.00[JPT][hapmap]
rs17115146	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17115155	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs476568	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs484064	0.83[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs490793	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs502701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506832	0.87[EUR][1000 genomes]
rs510824	0.89[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs513259	0.89[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs519401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs535415	0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs537307	0.89[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs546020	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs549622	0.94[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs550511	0.82[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs553453	0.89[CEU][hapmap];0.90[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs553508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[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]
rs561258	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs563921	0.94[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs564665	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs578962	0.88[EUR][1000 genomes]
rs579057	0.88[CEU][hapmap];0.90[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	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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
rs556204	C1orf177	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57577200-57595600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57588200-57596800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:57589400-57608600	Weak transcription	Fetal Intestine Large	intestine
5	chr1:57590600-57601400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:57590800-57597000	Weak transcription	NHDF-Ad	bronchial
7	chr1:57591200-57597000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:57592600-57596600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:57592600-57596800	Weak transcription	HMEC	breast
10	chr1:57592600-57597000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:57592800-57596800	Weak transcription	NHEK	skin
12	chr1:57593400-57597000	Weak transcription	Fetal Heart	heart
13	chr1:57595400-57600800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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