Variant report

Variant	rs28370782
Chromosome Location	chr12:40417167-40417168
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs13377779	1.00[AMR][1000 genomes]
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]
rs17465716	1.00[JPT][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489170	1.00[AMR][1000 genomes]
rs17489267	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489295	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489417	0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489459	1.00[JPT][hapmap]
rs17489466	1.00[AMR][1000 genomes]
rs17489480	1.00[JPT][hapmap]
rs17489522	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489583	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489666	1.00[JPT][hapmap]
rs17490013	1.00[JPT][hapmap]
rs17490578	1.00[JPT][hapmap]
rs17518014	1.00[JPT][hapmap]
rs17518050	1.00[JPT][hapmap]
rs17518141	0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518148	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518155	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518176	0.84[YRI][hapmap]
rs17518183	1.00[JPT][hapmap]
rs17518190	1.00[AMR][1000 genomes]
rs17518322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518329	0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518357	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518427	1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
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]
rs28370687	1.00[AMR][1000 genomes]
rs28370691	1.00[AMR][1000 genomes]
rs28370698	1.00[JPT][hapmap]
rs28370706	1.00[JPT][hapmap]
rs28370710	1.00[AMR][1000 genomes]
rs28370715	1.00[AMR][1000 genomes]
rs28370716	1.00[AMR][1000 genomes]
rs28370720	1.00[JPT][hapmap]
rs28370728	1.00[JPT][hapmap]
rs28370730	1.00[JPT][hapmap]
rs28370743	1.00[JPT][hapmap]
rs28370749	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370751	1.00[AMR][1000 genomes]
rs28370759	1.00[JPT][hapmap]
rs28370760	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370763	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370766	1.00[JPT][hapmap]
rs28370769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370770	1.00[JPT][hapmap]
rs28370775	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370777	1.00[JPT][hapmap]
rs28370778	1.00[JPT][hapmap]
rs28370781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370784	1.00[JPT][hapmap]
rs28370786	1.00[JPT][hapmap]
rs28370787	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370788	1.00[AMR][1000 genomes]
rs28370789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370791	1.00[YRI][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]
rs28740215	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28740216	1.00[AMR][1000 genomes]
rs56193998	1.00[AMR][1000 genomes]
rs57966079	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58812092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59404097	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59663144	1.00[AMR][1000 genomes]
rs60755503	1.00[AMR][1000 genomes]
rs61339615	0.92[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:5 , 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
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 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	chr12:40405800-40421000	Weak transcription	Left Ventricle	heart
5	chr12:40405800-40425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:40405800-40426000	Weak transcription	Pancreas	Pancrea
7	chr12:40406000-40423200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:40406600-40423200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:40406600-40425800	Weak transcription	Liver	Liver
10	chr12:40407800-40426000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:40409600-40426000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:40410000-40417200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:40410000-40422200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:40411000-40418800	Weak transcription	Aorta	Aorta
15	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:40411600-40418800	Weak transcription	Right Atrium	heart
18	chr12:40411600-40422000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:40411600-40424000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:40411600-40425600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:40411600-40426200	Weak transcription	Esophagus	oesophagus
22	chr12:40411800-40425200	Weak transcription	Fetal Intestine Small	intestine
23	chr12:40411800-40425600	Weak transcription	Fetal Intestine Large	intestine
24	chr12:40411800-40425600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:40411800-40426400	Weak transcription	Right Ventricle	heart
26	chr12:40412400-40417200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:40412400-40417400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:40412800-40417200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:40415000-40426000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:40416200-40425400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:40416600-40425400	Weak transcription	Psoas Muscle	Psoas
32	chr12:40416600-40441800	Weak transcription	Ovary	ovary
33	chr12:40416800-40417200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:40416800-40417200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr12:40416800-40417200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr12:40416800-40417200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:40416800-40417400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:40416800-40417400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:40417000-40417200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr12:40417000-40417200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:40417000-40417200	Enhancers	Brain Germinal Matrix	brain
42	chr12:40417000-40417200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:40417000-40417200	Enhancers	Lung	lung
44	chr12:40417000-40426000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:40417000-40426400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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