Variant report

Variant	rs13172149
Chromosome Location	chr5:14363446-14363447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11955578	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs11957060	0.88[CEU][hapmap]
rs11957857	0.83[EUR][1000 genomes]
rs13172877	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13188746	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13189406	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs154151	0.94[EUR][1000 genomes]
rs17304403	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185355	0.94[EUR][1000 genomes]
rs187667	0.91[EUR][1000 genomes]
rs247137	0.94[EUR][1000 genomes]
rs256412	0.91[EUR][1000 genomes]
rs28343	0.91[EUR][1000 genomes]
rs30766	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs30767	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs30768	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs30772	0.93[EUR][1000 genomes]
rs30773	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs30785	0.94[EUR][1000 genomes]
rs30786	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs30787	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs30788	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs30789	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs30790	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs30791	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs30793	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs30799	0.93[EUR][1000 genomes]
rs30800	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs30801	0.91[EUR][1000 genomes]
rs35860741	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36077682	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs378369	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs382403	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs389729	0.88[CEU][hapmap]
rs397319	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs40278	0.91[EUR][1000 genomes]
rs40572	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs42555	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs42556	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs434279	0.94[EUR][1000 genomes]
rs4702028	0.82[YRI][hapmap]
rs4702029	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71614085	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs730184	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs744048	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3383321	chr5:14363412-14363613	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14342800-14365200	Weak transcription	Small Intestine	intestine
2	chr5:14350400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:14353600-14366200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:14353600-14385200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr5:14354400-14374800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:14354600-14402400	Strong transcription	Liver	Liver
9	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
10	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr5:14355400-14365200	Strong transcription	HSMM	muscle
12	chr5:14355600-14375000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:14356000-14366200	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr5:14356400-14365400	Strong transcription	NHEK	skin
15	chr5:14356400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:14356600-14363800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:14356600-14365200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:14356800-14370200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:14356800-14376000	Strong transcription	HepG2	liver
20	chr5:14357000-14370400	Strong transcription	Fetal Intestine Small	intestine
21	chr5:14357000-14371200	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:14357000-14374000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:14357000-14376400	Strong transcription	NHLF	lung
24	chr5:14357000-14376600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr5:14357600-14365200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
27	chr5:14357800-14385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:14357800-14389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:14358000-14373800	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr5:14358000-14377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:14358000-14385800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:14358000-14389800	Strong transcription	Adipose Nuclei	Adipose
33	chr5:14358200-14366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:14358200-14366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:14358200-14375800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:14358200-14391600	Strong transcription	Primary B cells from cord blood	blood
37	chr5:14358400-14364800	Strong transcription	GM12878-XiMat	blood
38	chr5:14358400-14365000	Strong transcription	NH-A	brain
39	chr5:14358400-14366400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr5:14358400-14371200	Strong transcription	Fetal Brain Female	brain
41	chr5:14358400-14374200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:14358400-14374600	Strong transcription	Fetal Stomach	stomach
43	chr5:14358400-14385600	Strong transcription	Fetal Intestine Large	intestine
44	chr5:14358400-14392000	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:14358600-14364400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:14358600-14373600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:14358600-14374000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:14358600-14392600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:14358800-14364400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:14358800-14364400	Strong transcription	HMEC	breast

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