Variant report

Variant	rs28370775
Chromosome Location	chr12:40409678-40409679
allele	A/G
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
ENSG00000151229	Chromatin interaction
ENSG00000205592	Chromatin interaction
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13377779	1.00[AMR][1000 genomes]
rs17489170	1.00[AMR][1000 genomes]
rs17489267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489295	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489417	0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489466	1.00[AMR][1000 genomes]
rs17489522	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489583	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518141	0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518148	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518155	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518176	0.84[YRI][hapmap]
rs17518190	1.00[AMR][1000 genomes]
rs17518322	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518329	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518357	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518427	0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370687	1.00[AMR][1000 genomes]
rs28370691	1.00[AMR][1000 genomes]
rs28370710	1.00[AMR][1000 genomes]
rs28370715	1.00[AMR][1000 genomes]
rs28370716	1.00[AMR][1000 genomes]
rs28370749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370751	1.00[AMR][1000 genomes]
rs28370760	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370763	0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370781	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370782	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370787	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370788	1.00[AMR][1000 genomes]
rs28370789	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370791	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28740215	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28740216	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56193998	1.00[AMR][1000 genomes]
rs57966079	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58812092	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59404097	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59663144	1.00[AMR][1000 genomes]
rs60755503	1.00[AMR][1000 genomes]
rs61339615	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088130	1.00[AMR][1000 genomes]
rs74088192	1.00[AMR][1000 genomes]
rs74089321	1.00[AMR][1000 genomes]
rs74091033	1.00[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:46 , 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	chr12:40405600-40410400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:40405600-40417000	Weak transcription	Lung	lung
7	chr12:40405800-40410200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:40405800-40410800	Weak transcription	Aorta	Aorta
9	chr12:40405800-40410800	Weak transcription	Right Ventricle	heart
10	chr12:40405800-40411200	Weak transcription	NHLF	lung
11	chr12:40405800-40412800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:40405800-40414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
14	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
16	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:40406400-40410400	Enhancers	Fetal Intestine Large	intestine
18	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:40406600-40425800	Weak transcription	Liver	Liver
20	chr12:40406800-40410600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:40406800-40410800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:40406800-40410800	Weak transcription	Fetal Lung	lung
23	chr12:40406800-40410800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:40406800-40410800	Weak transcription	Right Atrium	heart
25	chr12:40407000-40410600	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:40407400-40410000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:40407600-40411200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:40409000-40409800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:40409000-40409800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr12:40409200-40410800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:40409200-40411200	Enhancers	Stomach Mucosa	stomach
33	chr12:40409200-40411600	Enhancers	NHDF-Ad	bronchial
34	chr12:40409400-40410000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:40409400-40410000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:40409400-40411800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:40409400-40412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:40409600-40410600	Weak transcription	Osteobl	bone
39	chr12:40409600-40411200	Weak transcription	Fetal Intestine Small	intestine
40	chr12:40409600-40411400	Enhancers	A549	lung
41	chr12:40409600-40412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:40409600-40412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:40409600-40412800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:40409600-40413000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:40409600-40414000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell

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