Variant report

Variant	rs299487
Chromosome Location	chr12:29716917-29716918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10400534	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10400541	0.95[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs10492312	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10771550	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771551	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771552	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10843445	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050284	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11050285	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050308	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12372765	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1326758	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs1409615	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs148898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1529908	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs159685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159687	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159689	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159690	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159694	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159695	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159696	0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs159697	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159698	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs159699	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs159700	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs159702	0.80[YRI][hapmap]
rs159713	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.91[YRI][hapmap]
rs159716	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs177254	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1863224	0.91[JPT][hapmap]
rs2081429	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2113879	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2113880	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[ASN][1000 genomes]
rs2162033	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2194819	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2209660	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2209661	0.91[JPT][hapmap]
rs2209662	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2225065	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2243623	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2254945	0.92[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288131	0.91[CEU][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2288230	0.86[ASN][1000 genomes]
rs2350532	0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs2710775	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766599	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766600	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2766601	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766602	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766604	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299444	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299445	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs299453	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299454	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299456	0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs299457	0.87[EUR][1000 genomes]
rs299458	0.83[ASN][1000 genomes]
rs299462	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299463	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299464	0.91[ASN][1000 genomes]
rs299465	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs299466	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs299467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299468	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299469	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs299470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299471	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299472	0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs299473	1.00[YRI][hapmap]
rs299475	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs299479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366998	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3910440	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3910441	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4931204	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57231427	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311193	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7959535	0.91[JPT][hapmap]
rs7960782	0.91[JPT][hapmap]
rs7965227	0.91[JPT][hapmap]
rs994171	0.83[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1053629	chr12:29680163-29826626	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29665400-29725400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:29700400-29719000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:29709800-29756200	Weak transcription	HMEC	breast
5	chr12:29710200-29717800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:29711400-29718200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:29711800-29720800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:29712600-29722200	Weak transcription	Colonic Mucosa	Colon
9	chr12:29712600-29734600	Weak transcription	Liver	Liver
10	chr12:29712800-29722200	Weak transcription	Brain Germinal Matrix	brain
11	chr12:29713200-29719800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:29713200-29719800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:29713200-29726400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:29713200-29726600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:29714200-29717400	Enhancers	Fetal Kidney	kidney
18	chr12:29714200-29717800	Enhancers	HSMMtube	muscle
19	chr12:29714400-29717400	Enhancers	Adipose Nuclei	Adipose
20	chr12:29714400-29717400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr12:29714400-29717600	Enhancers	NHLF	lung
22	chr12:29714400-29717800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:29714600-29717400	Enhancers	Fetal Heart	heart
24	chr12:29715000-29717200	Enhancers	Fetal Stomach	stomach
25	chr12:29715200-29717000	Enhancers	HUVEC	blood vessel
26	chr12:29715200-29717400	Enhancers	Fetal Muscle Leg	muscle
27	chr12:29715200-29717600	Enhancers	Left Ventricle	heart
28	chr12:29715200-29717600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:29715200-29717800	Enhancers	Colon Smooth Muscle	Colon
30	chr12:29715400-29718000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:29715400-29721400	Weak transcription	Esophagus	oesophagus
32	chr12:29715400-29722200	Weak transcription	Fetal Lung	lung
33	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:29715600-29717000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:29715600-29717000	Enhancers	Right Atrium	heart
36	chr12:29715600-29717400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:29715600-29717800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:29715800-29717000	Enhancers	Small Intestine	intestine
39	chr12:29715800-29717600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr12:29715800-29719000	Weak transcription	NH-A	brain
41	chr12:29715800-29724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:29716000-29717600	Enhancers	Spleen	Spleen
43	chr12:29716000-29718200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29716200-29717600	Enhancers	Aorta	Aorta
45	chr12:29716200-29717600	Enhancers	Psoas Muscle	Psoas
46	chr12:29716200-29717600	Genic enhancers	HSMM	muscle
47	chr12:29716200-29719400	Weak transcription	Osteobl	bone
48	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:29716400-29717000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:29716400-29717000	Active TSS	Rectal Mucosa Donor 29	rectum

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