Variant report

Variant	rs12425630
Chromosome Location	chr12:40408991-40408992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40402537-40410050..12:40703633-40711447	GM12878	blood:
2	12:40402537-40410050..12:40497414-40501128	K562	blood:
3	12:40402537-40410050..12:40687302-40691796	GM12878	blood:
4	12:40402537-40410050..12:40793507-40812339	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000151229	Chromatin interaction
ENSG00000205592	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10506143	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10506144	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11174631	0.86[AMR][1000 genomes]
rs11174697	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11175186	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11564108	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11564117	0.81[AMR][1000 genomes]
rs11564131	1.00[EUR][1000 genomes]
rs11564190	1.00[EUR][1000 genomes]
rs11564199	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11564216	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11564218	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422544	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12424040	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12424294	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12425561	1.00[EUR][1000 genomes]
rs12426378	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12426643	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12427022	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17458549	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs17461387	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17483919	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131081	1.00[EUR][1000 genomes]
rs28365169	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28365173	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28365206	1.00[EUR][1000 genomes]
rs28365689	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs28370637	0.84[AMR][1000 genomes]
rs28370664	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28370682	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28370830	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4767961	0.87[AMR][1000 genomes]
rs4767962	1.00[EUR][1000 genomes]
rs4767964	1.00[EUR][1000 genomes]
rs4768206	0.86[AMR][1000 genomes]
rs4768213	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs729215	1.00[AFR][1000 genomes];0.89[AMR][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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394000-40410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:40405400-40445200	Weak transcription	K562	blood
5	chr12:40405600-40409000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:40405600-40409200	Weak transcription	Hela-S3	cervix
7	chr12:40405600-40410400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:40405600-40417000	Weak transcription	Lung	lung
9	chr12:40405800-40409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:40405800-40409000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:40405800-40409000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:40405800-40409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:40405800-40409200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:40405800-40409200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:40405800-40409400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:40405800-40409400	Weak transcription	Small Intestine	intestine
17	chr12:40405800-40410200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:40405800-40410800	Weak transcription	Aorta	Aorta
19	chr12:40405800-40410800	Weak transcription	Right Ventricle	heart
20	chr12:40405800-40411200	Weak transcription	NHLF	lung
21	chr12:40405800-40412800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:40405800-40414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
24	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
26	chr12:40406000-40409000	Weak transcription	A549	lung
27	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr12:40406400-40410400	Enhancers	Fetal Intestine Large	intestine
29	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:40406600-40425800	Weak transcription	Liver	Liver
31	chr12:40406800-40409200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:40406800-40409200	Weak transcription	NHDF-Ad	bronchial
33	chr12:40406800-40409600	Enhancers	Fetal Intestine Small	intestine
34	chr12:40406800-40410600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:40406800-40410800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:40406800-40410800	Weak transcription	Fetal Lung	lung
37	chr12:40406800-40410800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:40406800-40410800	Weak transcription	Right Atrium	heart
39	chr12:40407000-40409000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:40407000-40410600	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:40407200-40409000	Weak transcription	Osteobl	bone
42	chr12:40407400-40410000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:40407600-40411200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:40407800-40409400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:40408200-40409200	Weak transcription	Stomach Mucosa	stomach
47	chr12:40408600-40409400	Weak transcription	Rectal Mucosa Donor 31	rectum

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