Variant report

Variant	rs3731750
Chromosome Location	chr2:179406003-179406004
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1001238	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10207436	0.84[JPT][hapmap]
rs10930831	0.84[JPT][hapmap]
rs12052983	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12693162	0.94[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13411588	0.84[JPT][hapmap]
rs1559908	0.84[JPT][hapmap]
rs1560221	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16866334	0.84[JPT][hapmap]
rs16866342	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16866400	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs16866420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1978580	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2042995	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2042996	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163009	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288322	0.84[JPT][hapmap]
rs2288571	0.85[JPT][hapmap]
rs2303536	0.84[JPT][hapmap]
rs2303537	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2303838	0.85[JPT][hapmap];0.82[TSI][hapmap]
rs2366751	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472751	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562845	0.88[TSI][hapmap]
rs2562848	0.80[MKK][hapmap]
rs2742351	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs35504893	0.95[ASN][1000 genomes]
rs36113194	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3731746	0.85[JPT][hapmap]
rs3731754	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs3752689	0.84[JPT][hapmap]
rs3769864	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3813250	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820978	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829746	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894020	0.84[JPT][hapmap]
rs4894029	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4894030	0.90[CHB][hapmap]
rs6704545	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs6712785	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6723399	0.87[ASN][1000 genomes]
rs6735077	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6739142	0.84[JPT][hapmap]
rs6753709	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7575643	0.84[JPT][hapmap]
rs7577862	0.84[JPT][hapmap]
rs7589679	0.84[JPT][hapmap]
rs7598228	0.83[JPT][hapmap]
rs7600176	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs8179648	0.90[JPT][hapmap]
rs890578	0.85[JPT][hapmap]
rs9288019	0.84[JPT][hapmap]
rs957875	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967507	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9808377	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9967820	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3731750	HOXD9	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
4	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
9	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:179389400-179408200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:179389400-179408800	Weak transcription	HMEC	breast
13	chr2:179389400-179410000	Weak transcription	Hela-S3	cervix
14	chr2:179389400-179412800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:179389400-179413000	Weak transcription	Fetal Brain Male	brain
16	chr2:179389400-179413400	Weak transcription	NH-A	brain
17	chr2:179389400-179416800	Weak transcription	Stomach Mucosa	stomach
18	chr2:179389400-179417200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:179389400-179417200	Weak transcription	NHDF-Ad	bronchial
20	chr2:179389400-179417200	Weak transcription	NHLF	lung
21	chr2:179389400-179428200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:179390600-179426400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:179391200-179419200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:179393800-179439800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:179394800-179412600	Strong transcription	Primary T cells from cord blood	blood
26	chr2:179394800-179413400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:179394800-179417600	Strong transcription	HSMMtube	muscle
28	chr2:179394800-179421600	Strong transcription	Left Ventricle	heart
29	chr2:179395400-179414200	Strong transcription	Fetal Thymus	thymus
30	chr2:179395400-179423000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:179395600-179414200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:179395600-179421600	Strong transcription	Fetal Heart	heart
33	chr2:179395800-179411800	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:179395800-179414000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:179395800-179414200	Strong transcription	Dnd41	blood
36	chr2:179396000-179406200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:179396000-179413800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:179396000-179414600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:179396000-179415800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:179396000-179417600	Strong transcription	HSMM	muscle
41	chr2:179396000-179422400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:179396000-179445400	Strong transcription	Right Ventricle	heart
43	chr2:179396200-179411600	Strong transcription	Adipose Nuclei	Adipose
44	chr2:179396200-179414200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:179396200-179414800	Strong transcription	Pancreas	Pancrea
46	chr2:179396200-179419800	Strong transcription	Fetal Intestine Large	intestine
47	chr2:179396200-179420200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:179396400-179411400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:179396400-179411400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:179396400-179412600	Strong transcription	Primary hematopoietic stem cells	blood

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