Variant report

Variant	rs6878879
Chromosome Location	chr5:118682789-118682790
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	chr5:118669449..118670965-chr5:118681990..118684958,2	K562	blood:
2	chr5:118675434..118678874-chr5:118679948..118684456,6	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10519585	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11957102	0.94[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1396609	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs17145230	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17145248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17145265	0.83[GIH][hapmap];0.85[JPT][hapmap]
rs17145294	1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17385413	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3797340	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3797342	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797343	0.85[JPT][hapmap]
rs6863311	0.86[ASN][1000 genomes]
rs6864305	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6869512	0.85[JPT][hapmap]
rs6870253	0.82[JPT][hapmap]
rs6876224	0.85[JPT][hapmap]
rs6877025	0.85[JPT][hapmap]
rs6882237	0.86[ASN][1000 genomes]
rs6883657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6884061	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6896553	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs73237292	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73237297	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73239278	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73239280	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7703408	0.91[EUR][1000 genomes]
rs7707470	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6878879	RAB31	trans	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118673200-118683600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:118673200-118683800	Weak transcription	Hela-S3	cervix
5	chr5:118673400-118683000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:118673800-118683400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
8	chr5:118674400-118689000	Weak transcription	Gastric	stomach
9	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:118676800-118691400	Weak transcription	Lung	lung
11	chr5:118677000-118686000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr5:118677200-118686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:118677800-118683400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:118678000-118690600	Weak transcription	NHEK	skin
15	chr5:118678200-118683400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:118678200-118684600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:118678800-118683600	Weak transcription	Adipose Nuclei	Adipose
18	chr5:118678800-118686400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr5:118679000-118683400	Weak transcription	K562	blood
20	chr5:118679000-118683400	Weak transcription	NHLF	lung
21	chr5:118679000-118690600	Weak transcription	Fetal Intestine Small	intestine
22	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:118679600-118683200	Weak transcription	Fetal Heart	heart
24	chr5:118679600-118683600	Weak transcription	Fetal Kidney	kidney
25	chr5:118679800-118683400	Weak transcription	NHDF-Ad	bronchial
26	chr5:118679800-118683800	Weak transcription	Fetal Lung	lung
27	chr5:118679800-118689400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:118680000-118683600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:118680200-118682800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:118680200-118683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:118680200-118683600	Weak transcription	Osteobl	bone
32	chr5:118680200-118683800	Weak transcription	Small Intestine	intestine
33	chr5:118680200-118690400	Weak transcription	Stomach Mucosa	stomach
34	chr5:118680200-118690600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:118680200-118690600	Weak transcription	Colonic Mucosa	Colon
36	chr5:118680400-118689000	Weak transcription	Placenta	Placenta
37	chr5:118680400-118690600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
39	chr5:118681000-118683000	Enhancers	Primary hematopoietic stem cells	blood
40	chr5:118681200-118683800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr5:118681600-118684000	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr5:118681600-118684800	Genic enhancers	Primary T cells from cord blood	blood
43	chr5:118681800-118683000	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr5:118681800-118683000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:118681800-118684000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr5:118681800-118685400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr5:118681800-118685400	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr5:118682000-118683000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:118682000-118684600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr5:118682000-118684600	Weak transcription	Duodenum Mucosa	Duodenum

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