Variant report

Variant	rs828647
Chromosome Location	chr6:72083997-72083998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GAT2-3	chr6:72082956-72084734	NONHSAT113496

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1192035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1192036	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1192039	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1192044	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1192046	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1192051	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1322763	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6923579	0.93[EUR][1000 genomes]
rs828637	1.00[AFR][1000 genomes]
rs828640	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs828641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs828643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs828646	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs828656	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs828658	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs828659	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs828661	0.92[EUR][1000 genomes]
rs828663	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431356	chr6:72083881-72085879	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72061600-72097000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:72071400-72085200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:72075400-72087200	Weak transcription	Fetal Heart	heart
4	chr6:72076000-72084000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:72076000-72093400	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:72076200-72103200	Weak transcription	Aorta	Aorta
7	chr6:72076600-72087600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:72076600-72090200	Weak transcription	Ovary	ovary
9	chr6:72077000-72084000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:72077600-72084000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:72077600-72085400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:72077600-72093400	Weak transcription	Brain Anterior Caudate	brain
13	chr6:72077600-72094800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:72077800-72087800	Weak transcription	Right Ventricle	heart
15	chr6:72077800-72088000	Weak transcription	Left Ventricle	heart
16	chr6:72077800-72093000	Weak transcription	Lung	lung
17	chr6:72077800-72093200	Weak transcription	Pancreas	Pancrea
18	chr6:72077800-72097000	Weak transcription	Psoas Muscle	Psoas
19	chr6:72077800-72097200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:72078200-72084000	Weak transcription	NHDF-Ad	bronchial
21	chr6:72078200-72095400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:72079800-72098800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:72080400-72084400	Strong transcription	HSMM	muscle
24	chr6:72081200-72084400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr6:72081200-72087800	Weak transcription	HSMMtube	muscle
26	chr6:72081400-72091400	Strong transcription	Hela-S3	cervix
27	chr6:72081600-72084400	Weak transcription	Fetal Brain Male	brain
28	chr6:72082000-72087000	Weak transcription	Fetal Kidney	kidney
29	chr6:72082200-72084000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:72082200-72090800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:72082400-72088000	Weak transcription	Liver	Liver
32	chr6:72082600-72093200	Weak transcription	Osteobl	bone
33	chr6:72082800-72085200	Weak transcription	HUVEC	blood vessel
34	chr6:72082800-72086200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:72083400-72084000	Enhancers	Colon Smooth Muscle	Colon
36	chr6:72083400-72084400	Enhancers	Adipose Nuclei	Adipose
37	chr6:72083400-72084600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:72083400-72087200	Enhancers	HMEC	breast
39	chr6:72083400-72094600	Weak transcription	Fetal Intestine Large	intestine
40	chr6:72083600-72084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr6:72083600-72084000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:72083600-72084400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:72083600-72084400	ZNF genes & repeats	A549	lung
44	chr6:72083600-72084600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:72083800-72084200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
46	chr6:72083800-72084200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:72083800-72084400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:72083800-72084400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:72083800-72084400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:72083800-72084400	Strong transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links