Variant report

Variant	rs1880090
Chromosome Location	chr6:34990968-34990969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:34990900-34991050	NHLF	lung:	n/a	n/a
2	BACH1	chr6:34990918-34991247	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
HSPE1P11	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1051115	0.85[CHB][hapmap]
rs13196785	0.85[CHB][hapmap]
rs13205210	0.85[CHB][hapmap]
rs13219307	0.85[CHB][hapmap]
rs2038740	0.83[MEX][hapmap]
rs2296361	0.85[CHB][hapmap]
rs2296362	0.85[CHB][hapmap]
rs2689089	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs3734261	0.85[CHB][hapmap]
rs3734266	0.85[CHB][hapmap]
rs4646933	0.85[CHB][hapmap]
rs6457796	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs6457797	0.85[CHB][hapmap]
rs67388064	0.91[EUR][1000 genomes]
rs6925175	0.85[CHB][hapmap]
rs7739385	0.85[CHB][hapmap]
rs7743949	0.85[CHB][hapmap]
rs7761391	0.85[CHB][hapmap]
rs820077	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs9368849	0.83[MEX][hapmap]
rs9462027	0.85[CHB][hapmap];0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1880090	TCP11	cis	lymphoblastoid	seeQTL
rs1880090	TAF11	cis	cerebellum	SCAN
rs1880090	HCK	trans	lymphoblastoid	seeQTL
rs1880090	C6orf89	cis	parietal	SCAN
rs1880090	PPIL1	cis	parietal	SCAN
rs1880090	NUDT3	cis	parietal	SCAN
rs1880090	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34926800-34992200	Weak transcription	Small Intestine	intestine
2	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:34979800-35002000	Weak transcription	GM12878-XiMat	blood
5	chr6:34982800-34991800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:34982800-34992200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:34983000-34991800	Weak transcription	HMEC	breast
8	chr6:34983600-34992000	Weak transcription	A549	lung
9	chr6:34983800-34992200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:34984800-34991000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:34985000-34991400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr6:34985400-34991000	Weak transcription	Hela-S3	cervix
13	chr6:34986000-34992200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:34986200-34991800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:34986200-34991800	Weak transcription	NHDF-Ad	bronchial
16	chr6:34986200-34991800	Weak transcription	NHLF	lung
17	chr6:34986200-34992000	Weak transcription	NHEK	skin
18	chr6:34986200-34992200	Weak transcription	Osteobl	bone
19	chr6:34986200-34996400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:34986200-35015000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:34986400-35011800	Weak transcription	Dnd41	blood
22	chr6:34986600-34991600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr6:34986600-34992400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:34986600-34993000	Weak transcription	Esophagus	oesophagus
25	chr6:34986800-35014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:34987000-34991200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:34987000-35009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:34987000-35015800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:34987200-34991800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:34987200-34992000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:34987200-34993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:34987400-34991800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:34987400-34991800	Weak transcription	HSMM	muscle
34	chr6:34987400-34992400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:34987400-34998600	Weak transcription	Primary B cells from cord blood	blood
36	chr6:34987400-34999200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr6:34987400-34999600	Weak transcription	Fetal Kidney	kidney
38	chr6:34987400-35015800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:34987600-34992200	Weak transcription	Fetal Brain Female	brain
40	chr6:34987800-34992000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:34987800-34993200	Enhancers	Psoas Muscle	Psoas
42	chr6:34988000-34991200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:34988000-34992000	Weak transcription	Brain Germinal Matrix	brain
44	chr6:34988000-34992600	Genic enhancers	Fetal Muscle Leg	muscle
45	chr6:34988200-34993600	Enhancers	Brain Angular Gyrus	brain
46	chr6:34988200-34994200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:34988400-34991000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:34988400-34991400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:34988400-34992400	Weak transcription	HepG2	liver
50	chr6:34988400-34993200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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