Variant report

Variant	rs34008599
Chromosome Location	chr6:5031159-5031160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:5030674..5031313-chr6:5057093..5058040,2	K562	blood:
2	chr6:4775660..4776622-chr6:5030960..5031503,2	MCF-7	breast:
3	chr6:5004308..5006000-chr6:5030652..5032441,2	K562	blood:
4	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:
5	chr6:5004317..5004944-chr6:5030555..5031426,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP1R3G-2	chr6:5031039-5031359	ENSG00000272142.1
2	lnc-PPP1R3G-2	chr6:5031039-5031247	NONHSAT107503

No data

Variant related genes	Relation type
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12332997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55796617	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56193336	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56346886	1.00[EUR][1000 genomes]
rs57093437	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58769332	0.83[EUR][1000 genomes]
rs59365793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73349204	1.00[AMR][1000 genomes]
rs73352376	1.00[AFR][1000 genomes]
rs73353056	0.86[EUR][1000 genomes]
rs73353059	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73353070	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73359952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73365168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73365181	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9504306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats 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
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027000-5031200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr6:5027000-5031200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:5027000-5032600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:5027000-5032800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:5027000-5032800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:5027000-5033000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:5027000-5033000	Weak transcription	Colonic Mucosa	Colon
8	chr6:5027000-5033200	Weak transcription	Esophagus	oesophagus
9	chr6:5027000-5036400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:5027200-5031400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:5027200-5031600	Enhancers	HepG2	liver
12	chr6:5027200-5032600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:5027200-5032600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:5027200-5032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:5027200-5032800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:5027200-5032800	Weak transcription	HMEC	breast
18	chr6:5027200-5033000	Weak transcription	Fetal Intestine Small	intestine
19	chr6:5027200-5033000	Weak transcription	Right Atrium	heart
20	chr6:5027200-5034600	Weak transcription	Fetal Thymus	thymus
21	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
22	chr6:5027400-5032800	Weak transcription	Fetal Stomach	stomach
23	chr6:5027400-5033200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:5029000-5031600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:5029400-5034200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:5029800-5033000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:5030400-5031600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:5030400-5032000	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:5030600-5034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:5030800-5031200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:5030800-5031200	Active TSS	Brain Anterior Caudate	brain
32	chr6:5030800-5031200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:5030800-5031200	Enhancers	Left Ventricle	heart
34	chr6:5030800-5031200	Enhancers	Ovary	ovary
35	chr6:5030800-5031200	Enhancers	Right Ventricle	heart
36	chr6:5030800-5031400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:5030800-5031400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:5030800-5031400	Enhancers	HUVEC	blood vessel
39	chr6:5030800-5031400	Enhancers	K562	blood
40	chr6:5030800-5031400	Enhancers	NHEK	skin
41	chr6:5030800-5031600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:5030800-5031600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:5030800-5031600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:5030800-5031600	Enhancers	Primary B cells from peripheral blood	blood
45	chr6:5030800-5031600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:5030800-5031600	Enhancers	Fetal Muscle Leg	muscle
47	chr6:5030800-5031800	Enhancers	Placenta	Placenta
48	chr6:5030800-5031800	Enhancers	Spleen	Spleen
49	chr6:5030800-5032000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:5030800-5032800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links