Variant report

Variant	rs888771
Chromosome Location	chr5:118621024-118621025
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:118620088..118622427-chr5:118650333..118654456,3	K562	blood:
2	chr5:118607071..118610754-chr5:118620607..118623123,4	K562	blood:
3	chr5:118620088..118622247-chr5:118651505..118654456,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10035514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10053596	1.00[CEU][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10463467	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10519579	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs13153732	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs13172935	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs13174838	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1394630	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs1422012	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504979	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504980	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1553543	0.90[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17145063	1.00[JPT][hapmap]
rs17145066	1.00[JPT][hapmap]
rs17145124	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs17145129	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17145142	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1966478	0.80[AFR][1000 genomes]
rs1966479	0.93[YRI][hapmap];0.91[AFR][1000 genomes]
rs2012594	0.83[ASN][1000 genomes]
rs34692285	0.86[ASN][1000 genomes]
rs35067404	0.86[ASN][1000 genomes]
rs35113297	0.86[ASN][1000 genomes]
rs35623432	0.86[ASN][1000 genomes]
rs35831154	0.86[ASN][1000 genomes]
rs35956442	0.86[ASN][1000 genomes]
rs4895188	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58196366	0.86[ASN][1000 genomes]
rs61643326	0.86[ASN][1000 genomes]
rs6865343	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874081	0.86[ASN][1000 genomes]
rs6877317	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879919	0.80[CEU][hapmap]
rs6884614	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6884625	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73247096	0.86[ASN][1000 genomes]
rs888768	0.83[ASN][1000 genomes]
rs888769	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs905831	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs9327095	0.91[CEU][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9327097	0.90[CEU][hapmap]
rs9327098	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462426	chr5:118465249-118621672	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv599564	chr5:118465249-118621672	ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1016595	chr5:118468658-118621672	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1024648	chr5:118608175-118678268	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118610600-118622600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:118610800-118626000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr5:118611200-118623200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:118611200-118625200	Weak transcription	Right Atrium	heart
5	chr5:118611400-118622600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:118611800-118623200	Weak transcription	HUVEC	blood vessel
7	chr5:118612000-118622400	Weak transcription	Lung	lung
8	chr5:118612000-118625200	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:118613200-118623400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:118613800-118626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:118614000-118623400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:118614400-118623200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:118615000-118622200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:118615000-118626200	Weak transcription	Spleen	Spleen
15	chr5:118615200-118621600	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr5:118615200-118622400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:118616800-118624600	Enhancers	Fetal Heart	heart
18	chr5:118617600-118622400	Enhancers	GM12878-XiMat	blood
19	chr5:118617600-118622600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:118618000-118621200	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr5:118618000-118622000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:118618000-118622600	Weak transcription	Fetal Lung	lung
23	chr5:118618400-118622400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr5:118618400-118627800	Weak transcription	Right Ventricle	heart
25	chr5:118618600-118622200	Weak transcription	Left Ventricle	heart
26	chr5:118618600-118622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:118618800-118622400	Weak transcription	Pancreas	Pancrea
28	chr5:118618800-118622600	Weak transcription	HMEC	breast
29	chr5:118618800-118623800	Weak transcription	Fetal Kidney	kidney
30	chr5:118619200-118623200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:118619400-118622600	Enhancers	Primary B cells from cord blood	blood
32	chr5:118619400-118622600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr5:118619400-118622600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:118619400-118622600	Weak transcription	Fetal Stomach	stomach
35	chr5:118619400-118628600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr5:118619600-118622600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr5:118619800-118621200	Enhancers	Placenta	Placenta
38	chr5:118619800-118622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:118619800-118629600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr5:118620000-118622400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:118620000-118622600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:118620000-118622800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:118620000-118625200	Weak transcription	Gastric	stomach
44	chr5:118620000-118629400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr5:118620200-118621800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr5:118620400-118621400	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr5:118620400-118622000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:118620400-118622400	Enhancers	A549	lung
49	chr5:118620400-118623200	Enhancers	Primary hematopoietic stem cells	blood
50	chr5:118620600-118621400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links