Variant report

Variant	rs17715086
Chromosome Location	chr12:29482006-29482007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1072724	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743652	0.82[CHB][hapmap]
rs10743656	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771514	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771517	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771521	0.81[ASN][1000 genomes]
rs10843376	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10843385	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843399	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10843401	0.81[ASN][1000 genomes]
rs11050147	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050149	0.82[EUR][1000 genomes]
rs11050168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12301475	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12578931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12581107	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1836861	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2016832	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2288128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2350315	0.80[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782510	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3948497	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4277150	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931171	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931174	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6487807	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7298031	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7299283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302986	0.81[ASN][1000 genomes]
rs7313552	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7315346	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7358667	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956305	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7959145	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7961943	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7964831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980218	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs986072	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers 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 miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17715086	RP11-996F15.2	cis	lung	GTEx
rs17715086	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs17715086	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29452800-29494200	Weak transcription	Lung	lung
3	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
4	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
7	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
8	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:29470000-29486400	Weak transcription	Psoas Muscle	Psoas
11	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:29470000-29500000	Weak transcription	K562	blood
13	chr12:29470800-29485800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:29470800-29492800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:29470800-29492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:29470800-29493400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:29470800-29493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:29470800-29496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
21	chr12:29471200-29491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:29471200-29493000	Weak transcription	Brain Substantia Nigra	brain
23	chr12:29471200-29494400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:29471400-29495800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:29471600-29492600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:29472200-29493800	Weak transcription	Left Ventricle	heart
27	chr12:29473800-29485400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:29473800-29493000	Weak transcription	HMEC	breast
29	chr12:29473800-29522600	Weak transcription	NHEK	skin
30	chr12:29474000-29493400	Weak transcription	HUVEC	blood vessel
31	chr12:29474200-29485200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:29474200-29489600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:29474200-29490600	Weak transcription	NH-A	brain
34	chr12:29474200-29493000	Weak transcription	Osteobl	bone
35	chr12:29474200-29494200	Weak transcription	NHDF-Ad	bronchial
36	chr12:29474400-29485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:29474400-29490600	Weak transcription	Liver	Liver
38	chr12:29474800-29493800	Weak transcription	Fetal Intestine Large	intestine
39	chr12:29475600-29489600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:29475800-29485000	Weak transcription	Adipose Nuclei	Adipose
41	chr12:29475800-29491200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:29475800-29493200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:29475800-29493400	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:29476000-29485000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr12:29476000-29485200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr12:29476000-29492200	Weak transcription	Placenta	Placenta
47	chr12:29476000-29496000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:29476200-29485600	Weak transcription	Dnd41	blood
50	chr12:29476200-29488600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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