Variant report

Variant	rs10201883
Chromosome Location	chr2:178471407-178471408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178469309..178471749-chr2:178504224..178506672,2	K562	blood:
2	chr2:178470776..178473144-chr6:142522946..142525040,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10171135	1.00[CHB][hapmap]
rs10181259	0.84[CEU][hapmap]
rs10201367	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497497	0.84[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10497499	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11679519	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11694013	0.86[EUR][1000 genomes]
rs11889272	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs12620285	0.88[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13014417	0.84[CEU][hapmap]
rs13025391	0.86[TSI][hapmap]
rs13025904	0.86[TSI][hapmap]
rs13028757	0.86[TSI][hapmap]
rs13431091	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1348851	0.84[CEU][hapmap]
rs1358326	0.86[TSI][hapmap]
rs1446839	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1527403	0.83[EUR][1000 genomes]
rs1534305	0.93[EUR][1000 genomes]
rs1918345	0.84[EUR][1000 genomes]
rs1997207	0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2091442	0.83[EUR][1000 genomes]
rs2222712	0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2695315	0.84[CEU][hapmap];1.00[TSI][hapmap]
rs4893967	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4893970	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4893973	0.93[EUR][1000 genomes]
rs4893979	0.81[EUR][1000 genomes]
rs5025340	0.83[EUR][1000 genomes]
rs57986285	0.80[EUR][1000 genomes]
rs58160847	0.81[EUR][1000 genomes]
rs6433688	0.86[TSI][hapmap]
rs6723031	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6723063	0.84[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6746233	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6756918	0.84[CEU][hapmap];0.95[EUR][1000 genomes]
rs7560737	0.86[TSI][hapmap]
rs7573345	0.84[EUR][1000 genomes]
rs7586934	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10201883	PRKRA	cis	parietal	SCAN
rs10201883	TTC30B	cis	parietal	SCAN
rs10201883	TTC30A	cis	cerebellum	SCAN
rs10201883	AGPS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462800-178475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:178463800-178475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
5	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:178468400-178482800	Weak transcription	Fetal Brain Male	brain
8	chr2:178469400-178471800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:178469400-178475000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:178469400-178475000	Weak transcription	Aorta	Aorta
11	chr2:178471000-178471600	Enhancers	GM12878-XiMat	blood
12	chr2:178471200-178471600	Active TSS	Fetal Kidney	kidney
13	chr2:178471200-178471600	Flanking Active TSS	HUVEC	blood vessel
14	chr2:178471200-178471800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:178471200-178471800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:178471200-178472400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr2:178471400-178471600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:178471400-178471800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:178471400-178471800	Enhancers	Fetal Muscle Leg	muscle
20	chr2:178471400-178471800	Enhancers	Fetal Stomach	stomach
21	chr2:178471400-178471800	Enhancers	HepG2	liver

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