Variant report

Variant	rs12473500
Chromosome Location	chr2:20539513-20539514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20531227..20533989-chr2:20538784..20541462,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10175853	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10187080	0.94[ASN][1000 genomes]
rs10192042	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10206974	0.96[ASN][1000 genomes]
rs1043400	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10460445	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460449	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460450	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10460451	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856797	0.94[ASN][1000 genomes]
rs11096654	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096659	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11888357	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895228	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11896241	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11898408	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11900127	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11902769	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11903745	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465832	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472685	0.86[ASN][1000 genomes]
rs12474897	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12478265	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393733	0.86[ASN][1000 genomes]
rs17612703	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2072464	0.87[ASN][1000 genomes]
rs2080190	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2348703	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2820	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34678899	0.85[ASN][1000 genomes]
rs3796066	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821218	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62123442	0.86[ASN][1000 genomes]
rs6748274	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72785217	0.87[ASN][1000 genomes]
rs72785218	0.87[ASN][1000 genomes]
rs72785278	0.87[ASN][1000 genomes]
rs72785282	0.86[ASN][1000 genomes]
rs72785297	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72785298	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72785300	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72785301	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72787406	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72787409	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72787411	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787415	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787433	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787499	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72787500	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72787501	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788905	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72788906	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7558385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558833	0.97[ASN][1000 genomes]
rs7563245	0.81[ASN][1000 genomes]
rs7579571	0.93[EUR][1000 genomes]
rs7582642	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7595266	0.87[ASN][1000 genomes]
rs9306890	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9306891	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005366	chr2:20478859-20542134	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20523000-20547600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:20524400-20546400	Weak transcription	NH-A	brain
3	chr2:20526000-20544800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:20527800-20544800	Weak transcription	Placenta	Placenta
5	chr2:20527800-20548200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:20527800-20549200	Weak transcription	Aorta	Aorta
7	chr2:20528200-20546600	Weak transcription	Hela-S3	cervix
8	chr2:20528600-20546400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:20530800-20540000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:20530800-20546200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:20531000-20544600	Weak transcription	Fetal Brain Male	brain
12	chr2:20531000-20549200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:20531200-20546400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:20531400-20546400	Weak transcription	Fetal Kidney	kidney
15	chr2:20531400-20547800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:20531800-20547400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:20532000-20542200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:20532000-20547400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:20532400-20542400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:20532400-20545400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:20533000-20541800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr2:20533400-20543800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:20533600-20539600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:20533800-20540000	Weak transcription	Dnd41	blood
25	chr2:20533800-20540200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:20533800-20540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:20533800-20545200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:20533800-20549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20534200-20542000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:20534400-20542000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:20534600-20540200	Enhancers	Fetal Heart	heart
32	chr2:20534600-20540200	Weak transcription	K562	blood
33	chr2:20534600-20542200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:20534800-20540000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:20534800-20547400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:20535000-20540200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:20535000-20545600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:20535000-20547400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr2:20535200-20546600	Weak transcription	NHEK	skin
40	chr2:20535400-20540200	Enhancers	Primary T cells from cord blood	blood
41	chr2:20536000-20539800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:20536200-20539800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:20536200-20542000	Weak transcription	GM12878-XiMat	blood
44	chr2:20536200-20543600	Weak transcription	Fetal Stomach	stomach
45	chr2:20536200-20545000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:20536200-20545800	Weak transcription	Fetal Lung	lung
47	chr2:20536200-20546200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:20536200-20546200	Weak transcription	Brain Angular Gyrus	brain
49	chr2:20536200-20546400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:20536200-20546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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