Variant report

Variant	rs2039624
Chromosome Location	chr9:71417919-71417920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10114785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10117744	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10117789	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10119445	1.00[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10121974	1.00[CEU][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10124098	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10869323	0.97[ASN][1000 genomes]
rs10869538	0.90[JPT][hapmap]
rs1107109	1.00[MEX][hapmap]
rs11143739	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11143755	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143975	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11143976	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11143977	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12336702	0.86[EUR][1000 genomes]
rs12337137	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes]
rs12338217	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes]
rs12340532	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs12341382	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341508	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12341625	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12345359	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs12348451	0.86[JPT][hapmap]
rs12349647	0.90[JPT][hapmap]
rs12350205	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes]
rs12351476	0.90[JPT][hapmap]
rs12351519	1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs12352746	0.90[JPT][hapmap]
rs1414945	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2027023	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28371821	0.90[AMR][1000 genomes]
rs28406181	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28444745	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28535486	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3750375	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs3750376	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes]
rs3763607	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs3829061	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs4237272	0.90[JPT][hapmap]
rs56994943	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58984094	1.00[EUR][1000 genomes]
rs61453631	0.86[EUR][1000 genomes]
rs61547334	1.00[AMR][1000 genomes]
rs6560418	1.00[EUR][1000 genomes]
rs7018568	1.00[MEX][hapmap]
rs7018854	0.89[JPT][hapmap]
rs7019202	0.80[JPT][hapmap]
rs7021259	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7024695	0.80[JPT][hapmap]
rs7024959	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7027620	1.00[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7035068	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7035892	0.80[JPT][hapmap]
rs7037674	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041194	1.00[AMR][1000 genomes]
rs7046642	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047250	0.90[JPT][hapmap]
rs7048275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73646761	1.00[EUR][1000 genomes]
rs7847379	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs7849727	0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7851905	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7852244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7855274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7859396	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7863960	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes]
rs7865800	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869689	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7870383	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7875472	1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap]
rs953036	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic 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	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1050741	chr9:71405224-71450033	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv540148	chr9:71405224-71450033	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71399000-71420200	Weak transcription	Fetal Stomach	stomach
2	chr9:71403200-71419800	Weak transcription	Pancreas	Pancrea
3	chr9:71404600-71431400	Weak transcription	HepG2	liver
4	chr9:71409200-71421000	Weak transcription	Placenta	Placenta
5	chr9:71410200-71419200	Weak transcription	Gastric	stomach
6	chr9:71410200-71419600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:71410200-71419800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:71410200-71428600	Weak transcription	Aorta	Aorta
9	chr9:71410400-71420200	Weak transcription	Stomach Mucosa	stomach
10	chr9:71414000-71420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:71414000-71437000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:71414000-71445000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:71415000-71418600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:71416600-71422000	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:71417000-71418200	Flanking Active TSS	GM12878-XiMat	blood
16	chr9:71417000-71418600	Enhancers	Duodenum Mucosa	Duodenum
17	chr9:71417200-71418400	Enhancers	Fetal Intestine Large	intestine
18	chr9:71417200-71418400	Enhancers	Fetal Intestine Small	intestine
19	chr9:71417200-71418600	Enhancers	Colonic Mucosa	Colon
20	chr9:71417400-71418000	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr9:71417400-71419000	Enhancers	Right Atrium	heart
22	chr9:71417400-71420400	Enhancers	Fetal Heart	heart
23	chr9:71417400-71420400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr9:71417400-71421800	Enhancers	Right Ventricle	heart
25	chr9:71417400-71423600	Enhancers	Left Ventricle	heart
26	chr9:71417600-71418000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:71417800-71418800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:71417800-71419000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr9:71417800-71419600	Weak transcription	Brain Germinal Matrix	brain
30	chr9:71417800-71420000	Weak transcription	Lung	lung

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