Variant report

Variant	rs1431721
Chromosome Location	chr1:239885810-239885811
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1014670	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10737838	0.87[AMR][1000 genomes]
rs10802793	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10802794	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs10802795	0.84[CEU][hapmap]
rs10802798	0.82[AMR][1000 genomes]
rs10925956	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs1155611	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs1155612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12403980	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12406493	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12407154	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12743042	0.82[AMR][1000 genomes]
rs12751235	0.91[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1431718	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1431719	0.88[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2217532	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2278642	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2278643	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2278644	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2355210	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2355237	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2355238	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2883621	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738436	0.88[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56266008	0.91[ASN][1000 genomes]
rs6429152	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6429153	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6429154	0.89[AMR][1000 genomes]
rs6657343	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6688537	0.92[ASN][1000 genomes]
rs6688548	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6694220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695600	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs714266	0.91[ASN][1000 genomes]
rs717227	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7511970	0.88[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7551919	0.84[ASN][1000 genomes]
rs891700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs961065	0.87[ASN][1000 genomes]
rs988231	0.86[EUR][1000 genomes];0.97[ASN][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	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239875400-239890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:239878200-239891000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239883400-239888200	Weak transcription	Pancreas	Pancrea
4	chr1:239884200-239887200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:239884600-239886200	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr1:239884600-239886600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:239884800-239887200	Weak transcription	Fetal Thymus	thymus
8	chr1:239884800-239887400	Weak transcription	Thymus	Thymus
9	chr1:239885000-239886000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr1:239885000-239894000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:239885400-239886000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:239885400-239886200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:239885400-239888000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:239885400-239888600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:239885600-239886000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:239885600-239886000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:239885600-239887600	Enhancers	Dnd41	blood
18	chr1:239885600-239905600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:239885800-239886400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:239885800-239887000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:239885800-239887200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:239885800-239888600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr1:239885800-239888600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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