Variant report

Variant	rs39617
Chromosome Location	chr5:14210897-14210898
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11133784	0.87[CHB][hapmap]
rs11743665	0.87[CHD][hapmap]
rs149123	0.88[ASN][1000 genomes]
rs151899	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs151900	0.88[ASN][1000 genomes]
rs151924	0.93[ASN][1000 genomes]
rs164109	0.81[JPT][hapmap]
rs164629	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs164862	0.86[JPT][hapmap]
rs164863	0.80[JPT][hapmap]
rs165095	0.81[JPT][hapmap]
rs16903264	0.95[JPT][hapmap]
rs171592	0.95[ASN][1000 genomes]
rs245445	0.87[ASN][1000 genomes]
rs248899	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26114	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26136	0.96[ASN][1000 genomes]
rs26137	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26280	0.87[CHB][hapmap]
rs26281	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs26289	0.84[ASN][1000 genomes]
rs27463	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28014	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs28030	0.88[ASN][1000 genomes]
rs30618	0.81[JPT][hapmap]
rs30621	0.82[CEU][hapmap]
rs30631	0.82[CEU][hapmap]
rs32340	0.89[JPT][hapmap]
rs32392	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32548	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32571	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs33004	0.93[ASN][1000 genomes]
rs33007	0.93[ASN][1000 genomes]
rs33027	0.81[ASN][1000 genomes]
rs352112	0.97[ASN][1000 genomes]
rs354286	0.82[CHB][hapmap];0.98[CHD][hapmap]
rs544588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556928	0.87[CHB][hapmap]
rs7380307	0.81[JPT][hapmap]

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	nsv516415	chr5:13788886-14210897	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv534466	chr5:13847044-14246208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv1830112	chr5:14147376-14222601	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14200600-14217000	Weak transcription	Fetal Brain Male	brain
2	chr5:14202200-14212600	Enhancers	Primary B cells from peripheral blood	blood
3	chr5:14203800-14214600	Enhancers	Fetal Thymus	thymus
4	chr5:14204000-14216800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:14205000-14214400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:14205200-14211400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:14205200-14212000	Weak transcription	Aorta	Aorta
8	chr5:14205400-14212000	Enhancers	Primary B cells from cord blood	blood
9	chr5:14205400-14212800	Weak transcription	Brain Anterior Caudate	brain
10	chr5:14205400-14213000	Weak transcription	Brain Angular Gyrus	brain
11	chr5:14205400-14214000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:14205400-14214200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:14205400-14215000	Enhancers	Fetal Intestine Large	intestine
14	chr5:14205400-14216000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:14205400-14218800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:14205600-14213000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:14205600-14213200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:14205600-14213400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr5:14205600-14216000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:14205800-14211600	Enhancers	HUVEC	blood vessel
21	chr5:14205800-14215600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:14206600-14211800	Enhancers	Fetal Lung	lung
23	chr5:14206800-14218800	Weak transcription	Esophagus	oesophagus
24	chr5:14207000-14212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:14207000-14212400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:14207600-14211400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr5:14207600-14214800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:14208400-14212400	Weak transcription	Primary T cells from cord blood	blood
29	chr5:14208400-14212600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:14208400-14213800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:14208800-14211200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:14208800-14211200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr5:14208800-14211400	Enhancers	NHDF-Ad	bronchial
34	chr5:14208800-14211600	Enhancers	HMEC	breast
35	chr5:14208800-14211800	Enhancers	Osteobl	bone
36	chr5:14208800-14212600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr5:14209000-14211000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:14209000-14211200	Enhancers	HSMMtube	muscle
39	chr5:14209000-14211600	Enhancers	NH-A	brain
40	chr5:14209000-14212400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:14209000-14214000	Enhancers	NHEK	skin
42	chr5:14209000-14214600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:14209000-14218000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:14209200-14211000	Enhancers	Liver	Liver
45	chr5:14209200-14211400	Enhancers	A549	lung
46	chr5:14209200-14212000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:14209200-14213200	Flanking Active TSS	GM12878-XiMat	blood
48	chr5:14209200-14214400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:14209200-14214600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr5:14209200-14214600	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links