Variant report

Variant	rs12223473
Chromosome Location	chr11:58890492-58890493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1048374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896948	1.00[CEU][hapmap]
rs10896954	1.00[CEU][hapmap]
rs11229802	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11229810	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229821	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229831	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229832	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11229836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11229838	1.00[EUR][1000 genomes]
rs11229841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs11229842	1.00[EUR][1000 genomes]
rs11229843	1.00[EUR][1000 genomes]
rs11229844	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11229847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11229853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11229871	1.00[CEU][hapmap]
rs11229891	1.00[CEU][hapmap]
rs11229905	1.00[CEU][hapmap]
rs12221768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes]
rs12222675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12223085	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12225532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12225972	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12275736	1.00[CEU][hapmap]
rs17153381	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154626	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2154627	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154964	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35732637	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742277	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349021	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969871	1.00[EUR][1000 genomes]
rs60519524	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60795438	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60883299	1.00[EUR][1000 genomes]
rs7951382	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv468578	chr11:58790628-58901763	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv555147	chr11:58790628-58901763	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:58876200-58891800	Weak transcription	Fetal Heart	heart
4	chr11:58876200-58892000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:58880800-58894800	ZNF genes & repeats	Dnd41	blood
6	chr11:58881600-58903600	Weak transcription	Hela-S3	cervix
7	chr11:58884000-58890800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:58884000-58894800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:58885200-58891600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:58886000-58898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:58886400-58893600	Strong transcription	Fetal Thymus	thymus
12	chr11:58886600-58890800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:58886600-58898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:58886800-58890800	Weak transcription	HSMM	muscle
15	chr11:58886800-58892000	Weak transcription	NHDF-Ad	bronchial
16	chr11:58886800-58893400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:58886800-58898400	Weak transcription	Osteobl	bone
18	chr11:58886800-58898800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:58886800-58901200	Weak transcription	NHLF	lung
20	chr11:58886800-58903400	Weak transcription	NHEK	skin
21	chr11:58887000-58890600	Weak transcription	Fetal Lung	lung
22	chr11:58887000-58890800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:58887000-58890800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr11:58887000-58891000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:58887000-58891200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:58887000-58891600	Weak transcription	HMEC	breast
27	chr11:58887000-58891600	Weak transcription	HUVEC	blood vessel
28	chr11:58887000-58891800	Weak transcription	Primary B cells from cord blood	blood
29	chr11:58887000-58891800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:58887000-58892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:58887000-58892800	Weak transcription	Fetal Intestine Large	intestine
32	chr11:58887000-58899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:58887000-58899000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:58887200-58891600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:58887800-58891000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:58887800-58894600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr11:58888200-58891600	Weak transcription	Fetal Kidney	kidney
38	chr11:58888200-58893800	Weak transcription	HepG2	liver
39	chr11:58888400-58890800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr11:58888400-58891200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:58888400-58891600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:58888400-58891600	Weak transcription	Fetal Muscle Leg	muscle
43	chr11:58888400-58892200	Strong transcription	A549	lung
44	chr11:58888400-58899400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:58889200-58890800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:58889800-58894600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr11:58890000-58890600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:58890000-58893000	Weak transcription	Fetal Brain Male	brain
49	chr11:58890000-58893600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:58890000-58894600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links