Variant report

Variant	rs12773340
Chromosome Location	chr10:38308911-38308912
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10827830	1.00[EUR][1000 genomes]
rs10827834	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827837	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10827838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011375	1.00[EUR][1000 genomes]
rs11011376	1.00[EUR][1000 genomes]
rs11011385	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011391	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11011428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011429	1.00[EUR][1000 genomes]
rs11011430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11011438	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11812927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813723	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11813932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11814622	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11816860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11817782	1.00[AFR][1000 genomes]
rs11818933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12240311	1.00[EUR][1000 genomes]
rs12241614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12242343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12245586	1.00[EUR][1000 genomes]
rs12248857	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12250395	1.00[EUR][1000 genomes]
rs12252754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256794	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12256916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12257902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12258024	1.00[EUR][1000 genomes]
rs12258128	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12260189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12260310	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262814	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12262927	1.00[EUR][1000 genomes]
rs12266728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12267847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12269398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12770231	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12777107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12779056	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2023432	1.00[EUR][1000 genomes]
rs34222428	1.00[EUR][1000 genomes]
rs34445730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34591573	1.00[EUR][1000 genomes]
rs34918037	1.00[EUR][1000 genomes]
rs34964888	1.00[EUR][1000 genomes]
rs35006520	1.00[EUR][1000 genomes]
rs35246660	1.00[EUR][1000 genomes]
rs35404142	1.00[EUR][1000 genomes]
rs57753536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60538050	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491210	1.00[EUR][1000 genomes]
rs71491212	1.00[EUR][1000 genomes]
rs71491214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491227	1.00[EUR][1000 genomes]
rs71491228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71491229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9651365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38300400-38319600	Weak transcription	Gastric	stomach
2	chr10:38300600-38318000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:38300600-38331600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:38300600-38336000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:38300600-38339400	Weak transcription	Psoas Muscle	Psoas
6	chr10:38300800-38322000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr10:38300800-38339200	Weak transcription	HSMMtube	muscle
8	chr10:38301200-38311200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:38301200-38320400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:38301200-38325000	Weak transcription	NHLF	lung
11	chr10:38301400-38310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:38301400-38314200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:38301400-38316600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:38301400-38318800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr10:38301600-38312800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr10:38301600-38320000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr10:38301800-38326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr10:38301800-38344400	Weak transcription	Hela-S3	cervix
19	chr10:38302000-38313000	Strong transcription	Brain Germinal Matrix	brain
20	chr10:38302400-38311000	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:38302400-38312200	Strong transcription	Fetal Thymus	thymus
22	chr10:38302400-38327400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:38302600-38314400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr10:38302800-38310000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr10:38302800-38311000	Strong transcription	Adipose Nuclei	Adipose
26	chr10:38302800-38311000	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr10:38302800-38316800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:38302800-38327200	Strong transcription	Fetal Intestine Large	intestine
29	chr10:38302800-38327400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:38303000-38313000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr10:38303000-38313200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:38303000-38316600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:38303200-38312800	Strong transcription	Placenta	Placenta
34	chr10:38303200-38313200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:38303200-38320200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:38303200-38326400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:38303200-38327800	Strong transcription	Primary B cells from cord blood	blood
38	chr10:38303400-38310000	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr10:38303400-38316800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:38303600-38310000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:38303800-38310600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr10:38303800-38318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:38304000-38310400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:38304200-38309800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:38304200-38326400	Strong transcription	Primary T cells from cord blood	blood
46	chr10:38304400-38309800	Strong transcription	NH-A	brain
47	chr10:38304600-38309000	Strong transcription	HMEC	breast
48	chr10:38304600-38311400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:38304600-38312200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:38304600-38314200	Weak transcription	Esophagus	oesophagus

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