Variant report

Variant	rs28370656
Chromosome Location	chr12:40407459-40407460
allele	C/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
ENSG00000205592	Chromatin interaction
ENSG00000188906	Chromatin interaction
ENSG00000151229	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10506145	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1086490	1.00[JPT][hapmap]
rs10877837	1.00[JPT][hapmap]
rs11174370	1.00[JPT][hapmap]
rs11564133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11564137	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11564139	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11564160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11564194	1.00[JPT][hapmap]
rs11564223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11564282	1.00[JPT][hapmap]
rs12312535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12371119	1.00[JPT][hapmap]
rs12810368	1.00[JPT][hapmap]
rs12827948	1.00[JPT][hapmap]
rs1482282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1491926	0.93[AFR][1000 genomes]
rs17442108	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17442304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17442469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17442756	1.00[JPT][hapmap]
rs17442805	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17443112	1.00[JPT][hapmap];0.93[AFR][1000 genomes]
rs17458299	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17458396	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17458403	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs17461082	1.00[CHB][hapmap]
rs17461492	0.93[AFR][1000 genomes]
rs17465400	0.93[AFR][1000 genomes]
rs17465519	0.85[AFR][1000 genomes]
rs17465540	0.85[AFR][1000 genomes]
rs17483628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17559478	1.00[JPT][hapmap]
rs2046929	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2086598	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2404346	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2404574	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2708404	1.00[JPT][hapmap]
rs28370644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28740188	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55707305	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55993200	0.93[AFR][1000 genomes]
rs7305377	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7306718	1.00[JPT][hapmap]
rs7484475	1.00[JPT][hapmap]
rs7969495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974522	1.00[JPT][hapmap];0.93[AFR][1000 genomes]
rs7974972	1.00[JPT][hapmap]
rs992851	1.00[JPT][hapmap]

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	chr12:40405200-40408600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr12:40405400-40408200	Enhancers	Stomach Mucosa	stomach
6	chr12:40405400-40445200	Weak transcription	K562	blood
7	chr12:40405600-40407800	Enhancers	Duodenum Mucosa	Duodenum
8	chr12:40405600-40409000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:40405600-40409200	Weak transcription	Hela-S3	cervix
10	chr12:40405600-40410400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:40405600-40417000	Weak transcription	Lung	lung
12	chr12:40405800-40407600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr12:40405800-40409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:40405800-40409000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:40405800-40409000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:40405800-40409200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:40405800-40409200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:40405800-40409200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:40405800-40409400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:40405800-40409400	Weak transcription	Small Intestine	intestine
21	chr12:40405800-40410200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:40405800-40410800	Weak transcription	Aorta	Aorta
23	chr12:40405800-40410800	Weak transcription	Right Ventricle	heart
24	chr12:40405800-40411200	Weak transcription	NHLF	lung
25	chr12:40405800-40412800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:40405800-40414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
28	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
30	chr12:40406000-40409000	Weak transcription	A549	lung
31	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:40406400-40410400	Enhancers	Fetal Intestine Large	intestine
33	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:40406600-40425800	Weak transcription	Liver	Liver
35	chr12:40406800-40409200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:40406800-40409200	Weak transcription	NHDF-Ad	bronchial
37	chr12:40406800-40409600	Enhancers	Fetal Intestine Small	intestine
38	chr12:40406800-40410600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:40406800-40410800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:40406800-40410800	Weak transcription	Fetal Lung	lung
41	chr12:40406800-40410800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:40406800-40410800	Weak transcription	Right Atrium	heart
43	chr12:40407000-40409000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:40407000-40410600	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:40407200-40407600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:40407200-40409000	Weak transcription	Osteobl	bone
47	chr12:40407400-40410000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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