Variant report

Variant	rs12086246
Chromosome Location	chr1:173958895-173958896
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10912701	0.87[AFR][1000 genomes]
rs10912711	0.92[AFR][1000 genomes]
rs10912712	0.93[AFR][1000 genomes]
rs12062801	0.91[AFR][1000 genomes]
rs12063273	0.92[AFR][1000 genomes]
rs12063296	0.89[AFR][1000 genomes]
rs12064818	0.81[AFR][1000 genomes]
rs12072553	0.93[AFR][1000 genomes]
rs12078645	0.95[AFR][1000 genomes]
rs1322781	0.86[AFR][1000 genomes]
rs997165	0.92[AFR][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv872550	chr1:173913804-173964206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173900000-173962400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr1:173900000-173966600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:173900000-173968200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:173900200-173966400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:173900400-173964600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:173900800-173963800	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:173901400-173962200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr1:173901600-173966400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:173901600-173966400	Strong transcription	Dnd41	blood
10	chr1:173904000-173966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:173905000-173962400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:173906000-173959000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:173906800-173959000	Strong transcription	Liver	Liver
14	chr1:173909800-173974200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:173915600-173977800	Weak transcription	Stomach Mucosa	stomach
16	chr1:173923400-173962400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:173929000-173962200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:173931200-173962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:173931200-173965600	Weak transcription	Small Intestine	intestine
21	chr1:173931200-173969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:173941000-173965000	Strong transcription	Fetal Thymus	thymus
23	chr1:173942200-173967400	Weak transcription	Fetal Heart	heart
24	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
25	chr1:173947000-173966000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:173949200-173970600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:173949400-173960000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:173949600-173965600	Weak transcription	Esophagus	oesophagus
29	chr1:173949600-173970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:173950200-173961800	Weak transcription	Aorta	Aorta
31	chr1:173950400-173960200	Weak transcription	Brain Angular Gyrus	brain
32	chr1:173950600-173973400	Weak transcription	Psoas Muscle	Psoas
33	chr1:173951400-173960000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:173951400-173960200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:173952200-173960000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:173952200-173967200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:173952800-173959800	Weak transcription	Right Ventricle	heart
38	chr1:173952800-173960000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:173952800-173960200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:173952800-173960600	Weak transcription	NHEK	skin
41	chr1:173952800-173962200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr1:173952800-173967600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:173953000-173960000	Weak transcription	Colonic Mucosa	Colon
44	chr1:173953200-173974200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:173953400-173960000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:173953400-173960000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:173953400-173960200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:173953800-173960000	Weak transcription	Brain Anterior Caudate	brain
49	chr1:173953800-173960000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:173953800-173960200	Weak transcription	Brain Substantia Nigra	brain

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