Variant report

Variant	rs1001238
Chromosome Location	chr2:179464527-179464528
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12052983	0.81[CHB][hapmap]
rs12693162	0.88[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1560221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16866342	0.85[CHB][hapmap]
rs16866400	1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.92[ASN][1000 genomes]
rs16866418	0.80[TSI][hapmap]
rs16866420	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1978580	0.81[CHB][hapmap]
rs2042995	0.88[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs2042996	0.88[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303537	0.81[CHB][hapmap]
rs2303828	0.83[TSI][hapmap]
rs2366751	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472751	0.94[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562834	0.80[TSI][hapmap]
rs2562845	0.91[TSI][hapmap]
rs2562848	0.81[MKK][hapmap]
rs2742351	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs35504893	0.86[ASN][1000 genomes]
rs36113194	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731750	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]
rs3731754	0.85[CHB][hapmap]
rs3769864	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3769866	0.86[CHB][hapmap]
rs3813250	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820978	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3829746	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4894029	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894030	0.90[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6704545	0.86[CHB][hapmap]
rs6712785	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735077	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6753709	0.82[CHB][hapmap]
rs7600176	0.82[CHB][hapmap]
rs8179648	0.80[JPT][hapmap]
rs957875	0.89[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs967507	0.86[CHB][hapmap]
rs9808377	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1000642	chr2:179438866-179503211	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1001238	HOXD9	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:179408000-179503000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:179411000-179466000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:179414800-179471800	Weak transcription	Brain Substantia Nigra	brain
5	chr2:179428400-179478600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:179430800-179480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:179435200-179469800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:179437600-179478800	Weak transcription	Esophagus	oesophagus
9	chr2:179437800-179465600	Strong transcription	Left Ventricle	heart
10	chr2:179438000-179467600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:179438200-179467200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr2:179438200-179474800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:179438400-179518200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:179440200-179474400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:179440400-179467600	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:179440600-179478800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:179440600-179494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:179440600-179505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:179440800-179468200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:179441400-179468600	Weak transcription	Gastric	stomach
21	chr2:179441400-179498800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:179441600-179495000	Weak transcription	Fetal Intestine Small	intestine
23	chr2:179441800-179469400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:179441800-179471600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:179442000-179484200	Weak transcription	Colonic Mucosa	Colon
26	chr2:179442200-179466400	Weak transcription	K562	blood
27	chr2:179442200-179476800	Weak transcription	Placenta	Placenta
28	chr2:179442600-179475800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:179442600-179478800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:179442800-179492000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:179442800-179493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:179443000-179471200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:179444800-179484400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:179447200-179467200	Strong transcription	Primary T cells from cord blood	blood
35	chr2:179449400-179472600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:179450000-179482400	Weak transcription	Small Intestine	intestine
37	chr2:179451000-179467600	Strong transcription	HSMMtube	muscle
38	chr2:179451200-179466200	Strong transcription	Right Ventricle	heart
39	chr2:179453600-179471200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:179455000-179467200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:179455200-179474200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:179455800-179472600	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:179456800-179468600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:179457000-179465600	Weak transcription	Lung	lung
45	chr2:179457000-179469400	Weak transcription	Spleen	Spleen
46	chr2:179457800-179468600	Weak transcription	Pancreas	Pancrea
47	chr2:179458000-179474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:179459000-179479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:179460600-179465600	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:179460800-179480200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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