Variant report

Variant	rs2550870
Chromosome Location	chr16:72070129-72070130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10048111	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10048144	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10400963	0.86[JPT][hapmap]
rs10492813	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs10492814	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1050361	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1050363	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10852511	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11075924	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs11643192	0.80[JPT][hapmap]
rs12162087	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12325266	0.81[JPT][hapmap]
rs12443622	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12446480	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12449073	0.86[JPT][hapmap]
rs12917999	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12924413	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12930205	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12930702	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12932845	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16973716	0.90[JPT][hapmap]
rs2070937	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2070939	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2072141	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2081222	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2081223	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236765	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2241411	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2287998	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287999	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288000	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288001	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288002	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2303285	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs251033	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2550035	0.86[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs2550038	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs2550868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2550869	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2550876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764311	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs3764314	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs3812984	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs3812986	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3844425	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3852781	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs3852782	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3852784	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3890860	0.89[ASN][1000 genomes]
rs3909541	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4238964	0.85[JPT][hapmap]
rs4788458	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4788609	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4788610	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs56139130	0.88[ASN][1000 genomes]
rs6499557	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6499562	0.90[JPT][hapmap]
rs7185840	0.89[ASN][1000 genomes]
rs7188962	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7189115	0.89[ASN][1000 genomes]
rs7189591	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7190994	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7192848	0.80[JPT][hapmap]
rs7199261	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7200854	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7201225	0.80[JPT][hapmap]
rs7201643	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7201866	0.92[ASN][1000 genomes]
rs7202268	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7203426	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7203821	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7350838	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7940	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs8044868	0.90[JPT][hapmap]
rs8052338	0.85[JPT][hapmap]
rs8052408	0.90[JPT][hapmap]
rs8053907	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8059437	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8182213	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9924964	0.94[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9926927	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9927526	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9928157	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9930890	0.83[ASN][1000 genomes]
rs9932951	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9936642	0.80[JPT][hapmap]
rs9938382	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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 target site	89 gene(s)	inside rSNPs	diseases
2	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72043600-72075200	Weak transcription	Fetal Brain Male	brain
2	chr16:72051400-72078600	Weak transcription	Fetal Kidney	kidney
3	chr16:72058200-72072200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:72058200-72076000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr16:72058200-72076000	Weak transcription	HSMMtube	muscle
6	chr16:72058200-72077000	Weak transcription	Colonic Mucosa	Colon
7	chr16:72058200-72078000	Weak transcription	Fetal Lung	lung
8	chr16:72059600-72084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:72060000-72073200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr16:72060000-72079200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr16:72060200-72075600	Weak transcription	Lung	lung
12	chr16:72060200-72075600	Weak transcription	Pancreas	Pancrea
13	chr16:72060200-72075800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:72060200-72075800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr16:72060200-72076200	Weak transcription	Brain Angular Gyrus	brain
16	chr16:72060200-72076200	Weak transcription	Placenta	Placenta
17	chr16:72060200-72076400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr16:72060200-72080000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
21	chr16:72060600-72075800	Weak transcription	Brain Germinal Matrix	brain
22	chr16:72061600-72075200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr16:72061600-72075800	Weak transcription	Brain Anterior Caudate	brain
24	chr16:72061600-72076200	Weak transcription	Fetal Intestine Small	intestine
25	chr16:72062000-72072000	Weak transcription	Ovary	ovary
26	chr16:72062000-72076000	Weak transcription	Colon Smooth Muscle	Colon
27	chr16:72062000-72076000	Weak transcription	Thymus	Thymus
28	chr16:72062200-72075400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr16:72062200-72075600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:72062200-72079600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr16:72062200-72080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:72062400-72075400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr16:72062400-72075800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr16:72062400-72075800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr16:72062400-72076000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr16:72062400-72076000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:72062400-72076000	Weak transcription	Spleen	Spleen
38	chr16:72062400-72076800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr16:72062400-72078000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr16:72062600-72075400	Weak transcription	Brain Hippocampus Middle	brain
41	chr16:72062600-72075600	Weak transcription	Aorta	Aorta
42	chr16:72062600-72075600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr16:72062600-72075800	Weak transcription	Primary B cells from cord blood	blood
44	chr16:72062600-72075800	Weak transcription	Fetal Brain Female	brain
45	chr16:72062600-72076000	Weak transcription	Adipose Nuclei	Adipose
46	chr16:72062600-72079800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr16:72062800-72076200	Weak transcription	Gastric	stomach
48	chr16:72063800-72079800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr16:72064000-72075600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:72064000-72075800	Weak transcription	Primary T cells from cord blood	blood

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