Variant report

Variant	rs11963289
Chromosome Location	chr6:142890457-142890458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIVEP2-7	chr6:142889285-142891213	NONHSAT115318

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11962041	0.87[AMR][1000 genomes]
rs11967100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11967976	0.87[AMR][1000 genomes]
rs11968504	0.87[AMR][1000 genomes]
rs1361481	1.00[AFR][1000 genomes]
rs17071860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34207438	1.00[AFR][1000 genomes]
rs9689935	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs988704	1.00[AFR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023426	chr6:142813845-142940262	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830827	chr6:142840734-143015005	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv520479	chr6:142869099-142908146	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142885200-142891000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:142887600-142892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr6:142887600-142892200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:142887600-142892200	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:142887600-142892600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:142887800-142890800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:142887800-142892000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:142887800-142892200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:142888000-142891400	Enhancers	HMEC	breast
10	chr6:142888000-142892800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:142888200-142892000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:142888200-142892200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:142888400-142891800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:142888400-142893400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:142888600-142892000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:142888800-142891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:142888800-142892000	Enhancers	Rectal Smooth Muscle	rectum
18	chr6:142889000-142891400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:142889200-142892200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:142889200-142892600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr6:142889200-142893600	Enhancers	Dnd41	blood
22	chr6:142889400-142891200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:142889400-142891800	Enhancers	Fetal Thymus	thymus
24	chr6:142889400-142892600	Enhancers	HSMM	muscle
25	chr6:142889400-142893200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:142889600-142890600	Enhancers	NHDF-Ad	bronchial
27	chr6:142889600-142890800	Enhancers	Colon Smooth Muscle	Colon
28	chr6:142889600-142891000	Enhancers	NHEK	skin
29	chr6:142889600-142891800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:142889600-142892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:142889600-142892200	Enhancers	HSMMtube	muscle
32	chr6:142889800-142890600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:142889800-142892000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:142889800-142892000	Enhancers	Osteobl	bone
35	chr6:142889800-142893400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:142890000-142891200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:142890000-142891600	Enhancers	Fetal Lung	lung
38	chr6:142890000-142892000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:142890000-142892200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr6:142890000-142892200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:142890200-142891400	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr6:142890200-142891400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:142890200-142892000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:142890200-142892400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:142890400-142890800	Flanking Active TSS	NH-A	brain
46	chr6:142890400-142891800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:142890400-142892000	Enhancers	Stomach Mucosa	stomach
48	chr6:142890400-142892200	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links