Variant report

Variant	rs11639556
Chromosome Location	chr16:12247810-12247811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11642386	0.81[JPT][hapmap]
rs11643074	0.82[AMR][1000 genomes]
rs11648816	0.81[JPT][hapmap]
rs12596703	0.93[JPT][hapmap]
rs12599107	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12708747	0.93[JPT][hapmap]
rs12924889	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12926900	0.81[JPT][hapmap]
rs13333662	0.93[JPT][hapmap]
rs13336687	0.81[JPT][hapmap]
rs16958964	0.81[JPT][hapmap]
rs2175020	0.93[JPT][hapmap]
rs34098770	0.91[EUR][1000 genomes]
rs34147612	0.89[EUR][1000 genomes]
rs34565142	0.88[EUR][1000 genomes]
rs34598762	0.89[EUR][1000 genomes]
rs35208076	0.87[EUR][1000 genomes]
rs35293822	0.86[EUR][1000 genomes]
rs3851011	0.81[JPT][hapmap]
rs3851012	0.81[JPT][hapmap]
rs4238614	0.80[TSI][hapmap]
rs4781180	0.81[JPT][hapmap]
rs8048589	0.81[JPT][hapmap]
rs8063329	0.81[JPT][hapmap]

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	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12229000-12249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:12229400-12248000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr16:12229400-12250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr16:12229800-12251400	Weak transcription	NHEK	skin
6	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:12231400-12251000	Weak transcription	Ovary	ovary
9	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
10	chr16:12232000-12248600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:12233600-12251000	Weak transcription	NHDF-Ad	bronchial
12	chr16:12234600-12248600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr16:12234600-12261600	Weak transcription	Aorta	Aorta
14	chr16:12234600-12265600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr16:12235400-12251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr16:12236200-12249400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:12236200-12250800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr16:12237800-12249600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:12242200-12248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:12242200-12248800	Weak transcription	Adipose Nuclei	Adipose
21	chr16:12242200-12251000	Weak transcription	HSMMtube	muscle
22	chr16:12242200-12252400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr16:12242200-12252400	Weak transcription	Left Ventricle	heart
24	chr16:12242200-12252600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr16:12242200-12252600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr16:12242200-12253800	Weak transcription	Right Atrium	heart
27	chr16:12242200-12255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:12242200-12261600	Weak transcription	Lung	lung
29	chr16:12242200-12262800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr16:12242400-12250600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:12242400-12252400	Weak transcription	Right Ventricle	heart
33	chr16:12242400-12252600	Weak transcription	Fetal Brain Female	brain
34	chr16:12242400-12252800	Weak transcription	Brain Anterior Caudate	brain
35	chr16:12242400-12255800	Weak transcription	Thymus	Thymus
36	chr16:12242400-12256400	Weak transcription	Fetal Kidney	kidney
37	chr16:12242400-12264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:12242400-12280600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:12242600-12248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:12243200-12255400	Weak transcription	Psoas Muscle	Psoas
41	chr16:12244000-12251200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr16:12244000-12252800	Weak transcription	Fetal Muscle Leg	muscle
43	chr16:12244400-12255800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr16:12244600-12248000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:12244600-12248600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr16:12244600-12249200	Weak transcription	Spleen	Spleen
47	chr16:12244600-12249400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr16:12244800-12248800	Weak transcription	Esophagus	oesophagus
49	chr16:12244800-12261200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr16:12245000-12249200	Weak transcription	GM12878-XiMat	blood

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