Variant report

Variant	rs159690
Chromosome Location	chr12:29730819-29730820
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29713752..29715262-chr12:29730590..29732837,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10400534	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10400541	0.96[EUR][1000 genomes]
rs10492312	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771550	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771551	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771552	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843445	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050284	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11050285	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050308	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1326758	0.98[EUR][1000 genomes]
rs148898	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1529908	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs159685	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159694	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs159695	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159696	0.98[EUR][1000 genomes]
rs159697	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159698	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159699	0.89[ASN][1000 genomes]
rs159700	0.85[ASN][1000 genomes]
rs177254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081429	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113879	0.91[ASN][1000 genomes]
rs2113880	0.91[ASN][1000 genomes]
rs2162033	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2194819	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243623	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254945	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288131	0.83[EUR][1000 genomes]
rs2288230	0.91[ASN][1000 genomes]
rs2350532	0.86[ASN][1000 genomes]
rs2710775	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766599	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766600	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766601	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766602	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766604	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299444	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs299445	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs299453	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299454	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs299456	0.88[EUR][1000 genomes]
rs299457	0.88[EUR][1000 genomes]
rs299458	0.81[ASN][1000 genomes]
rs299462	0.89[ASN][1000 genomes]
rs299463	0.89[ASN][1000 genomes]
rs299464	0.89[ASN][1000 genomes]
rs299465	0.89[ASN][1000 genomes]
rs299466	0.89[ASN][1000 genomes]
rs299467	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299468	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299469	0.84[AMR][1000 genomes]
rs299470	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299471	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs299472	0.86[ASN][1000 genomes]
rs299475	0.91[ASN][1000 genomes]
rs299479	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs299487	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366998	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3910440	0.84[EUR][1000 genomes]
rs3910441	0.83[EUR][1000 genomes]
rs4931204	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57231427	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311193	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29700400-29734000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:29709800-29756200	Weak transcription	HMEC	breast
3	chr12:29712600-29734600	Weak transcription	Liver	Liver
4	chr12:29713200-29731200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:29713200-29742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:29715400-29731200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:29716200-29764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:29717600-29734800	Weak transcription	NHLF	lung
9	chr12:29717600-29736400	Weak transcription	Psoas Muscle	Psoas
10	chr12:29717800-29732200	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:29720000-29731400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:29720000-29731800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:29720200-29735000	Weak transcription	NHDF-Ad	bronchial
14	chr12:29720200-29735800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:29720200-29743600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:29722400-29733600	Weak transcription	Ovary	ovary
17	chr12:29722400-29735400	Weak transcription	HSMMtube	muscle
18	chr12:29722600-29735200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:29722600-29736400	Weak transcription	Fetal Stomach	stomach
20	chr12:29722800-29735400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:29722800-29735800	Weak transcription	Fetal Kidney	kidney
22	chr12:29723000-29735200	Weak transcription	HSMM	muscle
23	chr12:29725600-29733400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:29725600-29735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:29725800-29735200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:29726000-29731000	Weak transcription	Hela-S3	cervix
27	chr12:29726000-29751400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:29726200-29731400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:29726200-29734600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:29726200-29735200	Weak transcription	Aorta	Aorta
31	chr12:29727000-29731400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:29727000-29735200	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:29727000-29735200	Weak transcription	Right Atrium	heart
34	chr12:29727200-29733800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:29727800-29735400	Weak transcription	Fetal Heart	heart
36	chr12:29728600-29733000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:29728600-29733600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:29728800-29735200	Weak transcription	Spleen	Spleen
39	chr12:29729000-29734000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:29729200-29731200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:29729400-29744000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:29729600-29731000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:29730200-29731800	Enhancers	Adipose Nuclei	Adipose
44	chr12:29730200-29732200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:29730200-29732400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr12:29730200-29732600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:29730400-29732000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:29730400-29736200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:29730600-29731200	Weak transcription	Small Intestine	intestine
50	chr12:29730600-29731800	Enhancers	HUVEC	blood vessel

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