Variant report

Variant	rs2133188
Chromosome Location	chr1:222813753-222813754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222812494..222814477-chr1:222837950..222840377,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11485123	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12063226	0.82[EUR][1000 genomes]
rs1391557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391558	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498382	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011666	0.86[ASW][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes]
rs17011686	0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17163337	0.81[JPT][hapmap]
rs17163450	0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs17163468	0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs1909195	0.83[AMR][1000 genomes]
rs1909197	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2030076	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088514	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270707	0.86[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2378604	0.87[EUR][1000 genomes]
rs2936020	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936023	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936049	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936051	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2936052	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2936054	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002129	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002148	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008614	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008615	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008616	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008618	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008622	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008625	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008629	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008637	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34433664	0.88[EUR][1000 genomes]
rs35507977	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3811465	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs61827168	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9441835	0.82[AMR][1000 genomes]
rs9441926	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv2603048	chr1:222812642-222814132	Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2133188	C1orf58	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
6	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:222794600-222814000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:222794600-222815000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:222799600-222815000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:222801000-222816600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:222801200-222815200	Strong transcription	HSMM	muscle
12	chr1:222801400-222816800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:222801600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:222801800-222815000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:222802000-222813800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:222802200-222816800	Weak transcription	Stomach Mucosa	stomach
17	chr1:222802400-222816600	Weak transcription	HMEC	breast
18	chr1:222802600-222816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:222802800-222816600	Weak transcription	GM12878-XiMat	blood
20	chr1:222803000-222816800	Weak transcription	Colonic Mucosa	Colon
21	chr1:222803200-222816400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:222803200-222816600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:222803800-222816600	Weak transcription	NHLF	lung
24	chr1:222804400-222817000	Weak transcription	Fetal Brain Male	brain
25	chr1:222805600-222814200	Weak transcription	HSMMtube	muscle
26	chr1:222805800-222816600	Weak transcription	Fetal Heart	heart
27	chr1:222805800-222817000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:222806400-222816600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:222806400-222816600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:222806400-222816600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:222806600-222816600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:222806600-222816600	Weak transcription	HUVEC	blood vessel
33	chr1:222806800-222816600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:222807000-222816400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:222807000-222816600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:222807000-222816600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:222807000-222816800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:222807000-222816800	Weak transcription	Right Ventricle	heart
39	chr1:222807200-222814600	Weak transcription	Fetal Brain Female	brain
40	chr1:222807200-222816600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:222807200-222816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:222807200-222816600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:222807200-222816800	Weak transcription	Brain Germinal Matrix	brain
44	chr1:222807400-222816600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:222807400-222816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:222807400-222816600	Weak transcription	Brain Substantia Nigra	brain
47	chr1:222807400-222817000	Weak transcription	Aorta	Aorta
48	chr1:222807600-222814600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:222807600-222816600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:222807600-222816600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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