Variant report

Variant	rs4912411
Chromosome Location	chr1:57177244-57177245
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10749709	0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10889002	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10889003	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206875	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11206891	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12134054	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12138351	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12402675	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12405291	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12759063	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2051040	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2143749	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2746342	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2746344	0.82[AMR][1000 genomes]
rs2796542	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4451572	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4561065	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4912408	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6588645	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6588646	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6588647	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6663750	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676950	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6688242	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6688263	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
rs4912411	C1orf175	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57166200-57178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:57170000-57181200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:57170200-57185000	Weak transcription	Liver	Liver
4	chr1:57173400-57181400	Weak transcription	Left Ventricle	heart
5	chr1:57173400-57184200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:57174800-57177400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:57175200-57178000	Enhancers	NH-A	brain
8	chr1:57175400-57178000	Enhancers	NHLF	lung
9	chr1:57175800-57178000	Enhancers	NHDF-Ad	bronchial
10	chr1:57175800-57178200	Enhancers	Osteobl	bone
11	chr1:57176000-57178000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:57176200-57178400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:57176200-57184000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:57176800-57180800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:57177000-57178000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:57177000-57178600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:57177000-57185000	Weak transcription	Fetal Heart	heart
18	chr1:57177200-57180800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:57177200-57180800	Weak transcription	NHEK	skin
20	chr1:57177200-57181000	Weak transcription	HSMM	muscle
21	chr1:57177200-57181200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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