Variant report

Variant	rs10164417
Chromosome Location	chr2:178444130-178444131
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	chr2:178440922..178442592-chr2:178443833..178445640,2	K562	blood:
2	chr2:178442079..178444998-chr2:178454524..178456659,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10165142	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171135	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs10172355	0.89[EUR][1000 genomes]
rs10180514	1.00[JPT][hapmap]
rs10181259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10184488	1.00[JPT][hapmap]
rs10190306	1.00[JPT][hapmap]
rs10191015	1.00[JPT][hapmap]
rs10195917	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10497497	0.84[CEU][hapmap]
rs10497504	0.84[CEU][hapmap]
rs10497505	1.00[JPT][hapmap]
rs10497506	1.00[JPT][hapmap]
rs10497509	1.00[JPT][hapmap]
rs10754987	1.00[JPT][hapmap]
rs10754988	1.00[JPT][hapmap]
rs10803911	1.00[JPT][hapmap]
rs10803912	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs10930788	1.00[JPT][hapmap]
rs10930793	1.00[JPT][hapmap]
rs10930796	1.00[JPT][hapmap]
rs11679519	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11691740	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11694988	0.92[CEU][hapmap]
rs11887886	0.80[EUR][1000 genomes]
rs11889272	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12478545	1.00[JPT][hapmap]
rs12988366	0.92[CEU][hapmap]
rs13014417	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs13431091	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13431105	0.92[CEU][hapmap]
rs1345138	0.84[CEU][hapmap]
rs1348851	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1374438	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1446837	1.00[JPT][hapmap]
rs1446838	1.00[JPT][hapmap]
rs1446839	0.84[CEU][hapmap]
rs1530965	1.00[JPT][hapmap]
rs16865191	1.00[JPT][hapmap]
rs16865322	1.00[JPT][hapmap]
rs16865324	1.00[JPT][hapmap]
rs16865337	1.00[JPT][hapmap]
rs16865359	1.00[JPT][hapmap]
rs16865376	1.00[JPT][hapmap]
rs16865377	1.00[JPT][hapmap]
rs1852530	0.92[CEU][hapmap]
rs1867905	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1901823	1.00[JPT][hapmap]
rs2167902	1.00[JPT][hapmap]
rs2178017	0.84[CEU][hapmap]
rs2218575	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2293475	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2364851	1.00[JPT][hapmap]
rs2364852	1.00[JPT][hapmap]
rs2695315	0.84[CEU][hapmap]
rs3754989	1.00[JPT][hapmap]
rs3813260	1.00[JPT][hapmap]
rs4144278	0.84[CEU][hapmap]
rs4243389	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs4402804	1.00[JPT][hapmap]
rs4585065	1.00[JPT][hapmap]
rs4893829	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs4893834	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4893835	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4893940	1.00[JPT][hapmap]
rs4893942	1.00[JPT][hapmap]
rs4893956	0.84[CEU][hapmap]
rs4893964	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893970	0.84[CEU][hapmap]
rs6433666	1.00[JPT][hapmap]
rs6433672	0.84[CEU][hapmap]
rs6433677	1.00[JPT][hapmap]
rs6710109	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6718769	0.85[EUR][1000 genomes]
rs6723014	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6723031	0.84[CEU][hapmap]
rs6723063	0.84[CEU][hapmap]
rs6725331	1.00[JPT][hapmap]
rs6732250	1.00[JPT][hapmap]
rs6737342	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6744488	1.00[JPT][hapmap]
rs6752528	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs6756918	0.84[CEU][hapmap]
rs7570297	1.00[JPT][hapmap]
rs7571386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582179	0.82[CEU][hapmap]
rs7585952	1.00[JPT][hapmap]
rs7588049	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs7594073	1.00[JPT][hapmap]
rs7601132	1.00[JPT][hapmap]
rs7604668	1.00[JPT][hapmap]
rs9288003	0.89[EUR][1000 genomes]
rs935426	0.84[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10164417	TTC30B	cis	parietal	SCAN
rs10164417	AGPS	cis	cerebellum	SCAN
rs10164417	OSBPL6	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178438000-178449800	Weak transcription	Pancreas	Pancrea
2	chr2:178443200-178445600	Enhancers	Fetal Heart	heart
3	chr2:178443400-178445800	Enhancers	Colon Smooth Muscle	Colon
4	chr2:178443600-178444200	Enhancers	HepG2	liver
5	chr2:178444000-178445400	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr2:178444000-178446000	Enhancers	Rectal Smooth Muscle	rectum

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