Variant report

Variant	rs12524219
Chromosome Location	chr6:38239285-38239286
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38238497..38240023-chr6:38248972..38251308,2	K562	blood:
2	chr6:38230666..38232627-chr6:38236052..38240073,5	MCF-7	breast:
3	chr6:38236548..38239476-chr6:38249471..38251086,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLO1-2	chr6:38239267-38239558	NONHSAT112311

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10484933	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12526138	1.00[AFR][1000 genomes]
rs12529300	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12529640	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16890465	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs16890468	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes]
rs16890511	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs16890522	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711526	0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4711530	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714127	1.00[AFR][1000 genomes]
rs4714135	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4714137	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714142	1.00[AFR][1000 genomes]
rs62397007	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62397011	0.83[AMR][1000 genomes]
rs62397015	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6929505	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7739762	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs9462426	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38208200-38255000	Weak transcription	Ovary	ovary
2	chr6:38220600-38241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:38223600-38256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
5	chr6:38224600-38255200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:38224800-38256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:38225000-38255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:38226600-38256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:38226600-38257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:38230200-38253400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:38230800-38241200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:38230800-38256000	Weak transcription	Right Atrium	heart
14	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
15	chr6:38231000-38250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:38232800-38241200	Weak transcription	Small Intestine	intestine
17	chr6:38233800-38241800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:38234400-38241600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:38235800-38240000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:38235800-38241800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:38236000-38239600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:38236000-38239800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:38236000-38241600	Enhancers	Brain Substantia Nigra	brain
24	chr6:38236000-38241600	Enhancers	NH-A	brain
25	chr6:38236000-38241800	Enhancers	HSMMtube	muscle
26	chr6:38236200-38239400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:38236200-38239800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:38236200-38239800	Enhancers	Adipose Nuclei	Adipose
29	chr6:38236400-38239600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:38236600-38239800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:38237000-38241200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:38237200-38239600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:38237200-38239800	Enhancers	Brain Anterior Caudate	brain
34	chr6:38237200-38240600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:38237200-38241400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:38237200-38241600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:38237200-38241800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:38237200-38241800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:38237200-38241800	Enhancers	Osteobl	bone
40	chr6:38237400-38239400	Enhancers	H9 Cell Line	embryonic stem cell
41	chr6:38237400-38239600	Enhancers	NHLF	lung
42	chr6:38237400-38241600	Enhancers	HSMM	muscle
43	chr6:38238000-38240800	Weak transcription	Fetal Heart	heart
44	chr6:38238000-38241800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:38238000-38241800	Enhancers	NHDF-Ad	bronchial
46	chr6:38238000-38250400	Weak transcription	HUVEC	blood vessel
47	chr6:38238200-38239400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:38238200-38239600	Weak transcription	Brain Angular Gyrus	brain
49	chr6:38238200-38240000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:38238200-38257000	Weak transcription	Aorta	Aorta

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