Variant report

Variant	rs28370778
Chromosome Location	chr12:40411392-40411393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs17442095	1.00[JPT][hapmap]
rs17442346	1.00[JPT][hapmap]
rs17442353	1.00[JPT][hapmap]
rs17442490	1.00[JPT][hapmap]
rs17442882	1.00[JPT][hapmap]
rs17458257	1.00[JPT][hapmap]
rs17458745	1.00[JPT][hapmap]
rs17458773	1.00[JPT][hapmap]
rs17458974	1.00[JPT][hapmap]
rs17460894	1.00[JPT][hapmap]
rs17460992	1.00[JPT][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489225	1.00[AMR][1000 genomes]
rs17489302	1.00[AMR][1000 genomes]
rs17489379	1.00[AMR][1000 genomes]
rs17489459	1.00[JPT][hapmap]
rs17489480	1.00[JPT][hapmap]
rs17489666	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17489715	1.00[AMR][1000 genomes]
rs17489722	1.00[AMR][1000 genomes]
rs17489889	1.00[AMR][1000 genomes]
rs17490013	1.00[JPT][hapmap]
rs17490418	1.00[AMR][1000 genomes]
rs17490578	1.00[AMR][1000 genomes]
rs17490585	1.00[AMR][1000 genomes]
rs17490599	1.00[AMR][1000 genomes]
rs17490620	1.00[AMR][1000 genomes]
rs17518014	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518050	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17518071	1.00[AMR][1000 genomes]
rs17518183	1.00[JPT][hapmap]
rs17518204	1.00[AMR][1000 genomes]
rs17518253	1.00[AMR][1000 genomes]
rs17518273	1.00[AMR][1000 genomes]
rs17518364	1.00[AMR][1000 genomes]
rs17518427	1.00[JPT][hapmap]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
rs17518770	1.00[AMR][1000 genomes]
rs17518805	1.00[AMR][1000 genomes]
rs17518992	1.00[AMR][1000 genomes]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
rs28365202	1.00[JPT][hapmap]
rs28370603	1.00[JPT][hapmap]
rs28370641	1.00[JPT][hapmap]
rs28370650	1.00[JPT][hapmap]
rs28370657	1.00[JPT][hapmap]
rs28370688	1.00[AMR][1000 genomes]
rs28370698	1.00[JPT][hapmap]
rs28370706	1.00[JPT][hapmap]
rs28370720	1.00[JPT][hapmap]
rs28370728	1.00[JPT][hapmap]
rs28370730	1.00[JPT][hapmap]
rs28370743	1.00[JPT][hapmap]
rs28370745	1.00[AMR][1000 genomes]
rs28370748	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370755	1.00[AMR][1000 genomes]
rs28370758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370759	1.00[JPT][hapmap]
rs28370766	1.00[JPT][hapmap]
rs28370768	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370770	1.00[JPT][hapmap]
rs28370776	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370777	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370782	1.00[JPT][hapmap]
rs28370783	1.00[AMR][1000 genomes]
rs28370784	1.00[JPT][hapmap]
rs28370786	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370792	1.00[JPT][hapmap]
rs28370801	1.00[JPT][hapmap]
rs28370811	1.00[JPT][hapmap]
rs28370825	1.00[JPT][hapmap]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[YRI][hapmap];1.00[AFR][1000 genomes];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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:40405400-40445200	Weak transcription	K562	blood
4	chr12:40405600-40417000	Weak transcription	Lung	lung
5	chr12:40405800-40412800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:40405800-40414000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
8	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
10	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:40406600-40425800	Weak transcription	Liver	Liver
13	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:40409200-40411600	Enhancers	NHDF-Ad	bronchial
15	chr12:40409400-40411800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr12:40409400-40412400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:40409600-40411400	Enhancers	A549	lung
18	chr12:40409600-40412600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:40409600-40412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:40409600-40412800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:40409600-40413000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:40409600-40414000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:40409800-40413000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:40410000-40411600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:40410000-40417200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:40410000-40422200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:40410200-40411400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:40410400-40411400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:40410400-40413000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:40410600-40411400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:40410600-40411400	Enhancers	Colon Smooth Muscle	Colon
33	chr12:40410800-40411400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:40410800-40411400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:40410800-40411600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:40410800-40411600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr12:40410800-40411600	Enhancers	Fetal Lung	lung
38	chr12:40410800-40411600	Enhancers	Rectal Smooth Muscle	rectum
39	chr12:40410800-40411600	Enhancers	Right Atrium	heart
40	chr12:40410800-40411800	Enhancers	Right Ventricle	heart
41	chr12:40411000-40411600	Enhancers	Osteobl	bone
42	chr12:40411000-40417000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:40411000-40418800	Weak transcription	Aorta	Aorta
44	chr12:40411200-40411600	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr12:40411200-40411600	Enhancers	NHLF	lung
46	chr12:40411200-40411800	Enhancers	Fetal Intestine Large	intestine
47	chr12:40411200-40411800	Enhancers	Fetal Intestine Small	intestine

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