Variant report

Variant	rs12236403
Chromosome Location	chr9:140417507-140417508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:140406492..140409440-chr9:140417122..140420049,2	MCF-7	breast:
2	chr9:140332825..140334847-chr9:140416477..140418783,2	MCF-7	breast:
3	chr9:140414817..140416805-chr9:140417183..140419334,2	K562	blood:
4	chr9:140416012..140417647-chr9:140422028..140424528,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10118305	1.00[CEU][hapmap]
rs11507679	1.00[MEX][hapmap]
rs11507687	1.00[CHD][hapmap]
rs11522284	1.00[CHD][hapmap]
rs11541259	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs11791683	1.00[CEU][hapmap]
rs12156648	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs12788	1.00[AMR][1000 genomes]
rs13284456	1.00[CHD][hapmap]
rs1753858	1.00[CEU][hapmap]
rs17855638	1.00[CEU][hapmap]
rs2298171	1.00[CHD][hapmap]
rs28563072	1.00[CHD][hapmap]
rs28657895	1.00[CHD][hapmap]
rs28859278	1.00[CHD][hapmap]
rs3750384	1.00[CHD][hapmap]
rs57983917	1.00[AMR][1000 genomes]
rs58298832	1.00[AMR][1000 genomes]
rs58445783	1.00[AMR][1000 genomes]
rs58833156	1.00[AMR][1000 genomes]
rs59804638	1.00[AMR][1000 genomes]
rs60289189	1.00[AMR][1000 genomes]
rs61609571	1.00[AMR][1000 genomes]
rs61729741	1.00[AMR][1000 genomes]
rs7029134	1.00[CHD][hapmap]
rs73565597	1.00[AMR][1000 genomes]
rs73565600	1.00[AMR][1000 genomes]
rs73567224	1.00[AMR][1000 genomes]
rs73568105	1.00[AMR][1000 genomes]
rs73568112	1.00[AMR][1000 genomes]
rs73569746	1.00[AMR][1000 genomes]
rs73570047	1.00[AMR][1000 genomes]
rs73570096	1.00[AMR][1000 genomes]
rs73574129	1.00[AMR][1000 genomes]
rs73581585	1.00[AMR][1000 genomes]
rs73581598	1.00[AMR][1000 genomes]
rs73583524	1.00[AMR][1000 genomes]
rs73583537	1.00[AMR][1000 genomes]
rs73583550	1.00[AMR][1000 genomes]
rs7866456	1.00[MEX][hapmap]
rs821314	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs872341	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs9410118	1.00[AMR][1000 genomes]
rs9695196	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894442	chr9:139544437-140462099	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
3	nsv894474	chr9:139694521-140432318	Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
4	nsv894487	chr9:139725120-140449582	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
5	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
6	nsv894502	chr9:139823670-140487108	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv894523	chr9:139860631-140462099	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
8	nsv894564	chr9:139906359-140432318	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
9	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
10	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
11	nsv1047563	chr9:140219047-140560852	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv540357	chr9:140219047-140560852	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv531602	chr9:140240417-140535223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	diseases
14	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
15	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
16	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
17	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
18	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
19	nsv831762	chr9:140338779-140514107	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	n/a
20	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
21	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
22	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
23	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
24	nsv616022	chr9:140372570-140523429	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	n/a
25	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
26	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
27	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
28	nsv894663	chr9:140382705-140454791	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
29	nsv540362	chr9:140401645-140452700	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	n/a
30	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
31	nsv540363	chr9:140408112-140447920	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
32	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
33	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
34	nsv616024	chr9:140414410-140536098	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140376800-140444000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:140377000-140437000	Weak transcription	Left Ventricle	heart
3	chr9:140377200-140420200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:140388400-140425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:140392000-140425800	Weak transcription	Primary T cells from cord blood	blood
6	chr9:140393000-140417800	Weak transcription	Fetal Brain Female	brain
7	chr9:140393000-140429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:140394000-140419800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:140394000-140429200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:140396400-140429200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:140404200-140420000	Weak transcription	Brain Anterior Caudate	brain
12	chr9:140404200-140429200	Weak transcription	Aorta	Aorta
13	chr9:140406800-140420000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:140408600-140444400	Weak transcription	Esophagus	oesophagus
15	chr9:140409800-140420000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:140410000-140427200	Weak transcription	Stomach Mucosa	stomach
17	chr9:140410000-140429200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:140410200-140418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:140411000-140429000	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:140411200-140444200	Weak transcription	Right Atrium	heart
21	chr9:140413600-140419400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:140413800-140418200	Strong transcription	Ovary	ovary
23	chr9:140414000-140422000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:140414600-140429200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:140414600-140438400	Weak transcription	Colonic Mucosa	Colon
26	chr9:140414800-140418600	Weak transcription	Fetal Stomach	stomach
27	chr9:140415000-140425800	Weak transcription	Primary B cells from cord blood	blood
28	chr9:140416000-140429200	Weak transcription	Brain Angular Gyrus	brain
29	chr9:140416200-140417600	Weak transcription	Liver	Liver
30	chr9:140416200-140418600	Weak transcription	Adipose Nuclei	Adipose
31	chr9:140416200-140425400	Weak transcription	Fetal Intestine Small	intestine
32	chr9:140416200-140429200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:140416400-140418600	Weak transcription	Spleen	Spleen
34	chr9:140416400-140419600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr9:140416400-140419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr9:140416400-140420000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:140416400-140424800	Weak transcription	Fetal Muscle Leg	muscle
38	chr9:140416400-140429000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:140416400-140429000	Weak transcription	Lung	lung
40	chr9:140416400-140429200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:140416400-140429200	Weak transcription	Brain Hippocampus Middle	brain
42	chr9:140416400-140429200	Weak transcription	Brain Substantia Nigra	brain
43	chr9:140416400-140429200	Weak transcription	Right Ventricle	heart
44	chr9:140417000-140418800	Strong transcription	Gastric	stomach
45	chr9:140417400-140417600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:140417400-140417600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:140417400-140417600	Genic enhancers	Pancreas	Pancrea
48	chr9:140417400-140417800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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