Variant report

Variant	rs17008208
Chromosome Location	chr2:72693535-72693536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1000523	1.00[JPT][hapmap]
rs10209861	1.00[JPT][hapmap]
rs10496184	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10496185	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs11126367	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11126369	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1123199	1.00[JPT][hapmap]
rs11675264	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11675268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11680197	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11685876	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11689339	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs11689707	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11695000	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11695629	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11884162	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11887356	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs11892598	0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11897200	0.89[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11903453	0.81[YRI][hapmap]
rs11903908	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs11903912	1.00[GIH][hapmap]
rs1517179	0.82[YRI][hapmap]
rs17008015	0.87[LWK][hapmap];0.82[YRI][hapmap]
rs17008057	0.92[YRI][hapmap]
rs17008082	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17008143	0.89[YRI][hapmap]
rs17008186	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17008188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17008241	0.85[CEU][hapmap]
rs17008293	0.85[CEU][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs17263172	1.00[CEU][hapmap]
rs17725024	1.00[JPT][hapmap]
rs1949377	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2109963	1.00[JPT][hapmap]
rs2901190	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4507127	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs4508623	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs55728837	0.83[AFR][1000 genomes]
rs55747300	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55825364	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55939880	0.84[AFR][1000 genomes]
rs56184446	0.84[AFR][1000 genomes]
rs56718524	0.87[AFR][1000 genomes]
rs56777837	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58582296	0.87[AFR][1000 genomes]
rs58967293	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59176504	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59881252	0.85[AFR][1000 genomes]
rs60325013	0.82[EUR][1000 genomes]
rs60563535	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60580301	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs632670	0.85[YRI][hapmap]
rs634929	0.85[YRI][hapmap]
rs6546755	1.00[JPT][hapmap]
rs6546761	0.84[YRI][hapmap]
rs6546771	0.94[AFR][1000 genomes]
rs66489235	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66539158	0.84[AFR][1000 genomes]
rs66560019	0.87[AFR][1000 genomes]
rs6711442	0.81[YRI][hapmap]
rs6713712	0.85[CEU][hapmap]
rs67166018	0.80[AFR][1000 genomes]
rs6719255	1.00[JPT][hapmap]
rs6723136	1.00[GIH][hapmap]
rs6727580	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6733532	1.00[GIH][hapmap]
rs6733538	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6739768	0.85[CEU][hapmap]
rs6740390	0.84[CEU][hapmap]
rs67491855	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6755440	0.82[YRI][hapmap]
rs6756070	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6758324	1.00[GIH][hapmap]
rs6758689	1.00[GIH][hapmap]
rs678684	0.85[YRI][hapmap]
rs67970313	0.81[EUR][1000 genomes]
rs688433	0.85[YRI][hapmap]
rs72845175	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7557942	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7559116	1.00[GIH][hapmap]
rs7561471	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7569059	0.81[AFR][1000 genomes]
rs7571483	0.85[AFR][1000 genomes]
rs7571517	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7575050	0.89[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7577244	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7583268	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7591608	0.82[AFR][1000 genomes]
rs7604083	0.85[CEU][hapmap]
rs7604818	1.00[GIH][hapmap];0.91[TSI][hapmap]
rs7607353	1.00[GIH][hapmap];0.82[YRI][hapmap]
rs764766	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9678682	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv999179	chr2:72561463-72761103	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv582208	chr2:72690622-72835886	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17008208	INO80B	cis	parietal	SCAN
rs17008208	AUP1	cis	parietal	SCAN
rs17008208	SFXN5	cis	parietal	SCAN
rs17008208	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72672000-72702200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:72680800-72702000	Weak transcription	Fetal Stomach	stomach
3	chr2:72685600-72702000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:72689000-72694400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr2:72689800-72702200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:72690000-72702200	Weak transcription	Pancreas	Pancrea
7	chr2:72690400-72702200	Weak transcription	Fetal Kidney	kidney
8	chr2:72690800-72695800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:72691200-72694200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:72691200-72697600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:72691200-72702000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:72691200-72702000	Weak transcription	Right Ventricle	heart
13	chr2:72691400-72693800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:72691400-72694400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:72691400-72702400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:72691400-72712600	Weak transcription	Osteobl	bone
17	chr2:72691400-72724200	Weak transcription	Psoas Muscle	Psoas
18	chr2:72691400-72726400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:72691600-72693600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:72691600-72694000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:72691600-72694200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:72691600-72694200	Weak transcription	HMEC	breast
23	chr2:72691600-72694400	Weak transcription	A549	lung
24	chr2:72691600-72694800	Weak transcription	Primary T cells from cord blood	blood
25	chr2:72691600-72695000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:72691600-72696200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:72691600-72698800	Weak transcription	Fetal Heart	heart
28	chr2:72691600-72699000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:72691600-72702000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:72691600-72702200	Weak transcription	Aorta	Aorta
31	chr2:72691600-72702200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:72691600-72702200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:72691600-72702200	Weak transcription	Lung	lung
34	chr2:72691600-72702400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:72691600-72702400	Weak transcription	NHEK	skin
36	chr2:72691600-72707600	Weak transcription	Brain Angular Gyrus	brain
37	chr2:72691600-72724200	Weak transcription	HUVEC	blood vessel
38	chr2:72691600-72741800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:72691800-72694000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:72691800-72694000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:72691800-72694200	Weak transcription	Fetal Intestine Large	intestine
42	chr2:72691800-72694400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:72691800-72702000	Weak transcription	Brain Anterior Caudate	brain
44	chr2:72691800-72702000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:72691800-72702200	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:72691800-72702200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:72691800-72702200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:72691800-72702200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:72692400-72694200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:72692400-72694400	Weak transcription	Fetal Brain Male	brain

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