Variant report

Variant	rs535490
Chromosome Location	chr6:106564434-106564435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106544729..106547210-chr6:106561631..106564573,3	K562	blood:
2	chr6:106560644..106566595-chr6:106567704..106572815,8	K562	blood:
3	chr6:106560146..106562675-chr6:106563041..106565107,2	K562	blood:
4	chr6:106562714..106568673-chr6:106569146..106572965,6	K562	blood:
5	chr6:106562594..106564776-chr6:106574919..106578759,3	K562	blood:

Variant related genes	Relation type
ENSG00000057657	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs541217	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs567826	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58926232	0.95[AFR][1000 genomes]
rs9486284	0.86[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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1018270	chr6:106531658-106908606	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS 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 target site	34 gene(s)	inside rSNPs	diseases
6	nsv538399	chr6:106531658-106908606	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1832544	chr6:106539914-106642993	Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1035110	chr6:106557281-106802212	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv538400	chr6:106557281-106802212	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106546800-106567000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:106553600-106584000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:106554600-106566800	Weak transcription	Hela-S3	cervix
4	chr6:106555400-106565000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:106556400-106567400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:106557200-106567200	Weak transcription	Fetal Intestine Large	intestine
7	chr6:106557600-106567400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:106559200-106567200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:106559200-106574200	Weak transcription	Small Intestine	intestine
10	chr6:106559600-106567200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr6:106560200-106567800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:106560800-106567200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:106561000-106564800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:106561400-106567400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:106561600-106567000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:106561800-106564800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr6:106561800-106564800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:106562000-106564600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:106562000-106567400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:106562400-106565000	Enhancers	Placenta	Placenta
21	chr6:106562600-106567200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:106562800-106565200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:106563000-106565000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:106563000-106567400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:106563200-106564600	Enhancers	Fetal Muscle Leg	muscle
26	chr6:106563200-106564600	Enhancers	GM12878-XiMat	blood
27	chr6:106563200-106565000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:106563200-106565000	Enhancers	HMEC	breast
29	chr6:106563200-106567400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:106563200-106567600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr6:106563400-106564800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:106563400-106566200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:106563400-106567000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:106563600-106564800	Enhancers	NHEK	skin
35	chr6:106563600-106565400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:106563600-106567400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:106563600-106567400	Weak transcription	HSMM	muscle
38	chr6:106563800-106564600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:106563800-106564600	Enhancers	Brain Cingulate Gyrus	brain
40	chr6:106563800-106564600	Enhancers	Brain Substantia Nigra	brain
41	chr6:106563800-106564600	Enhancers	Esophagus	oesophagus
42	chr6:106563800-106564600	Enhancers	Lung	lung
43	chr6:106563800-106564800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:106564000-106564600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:106564000-106564600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr6:106564000-106564600	Enhancers	Fetal Heart	heart
47	chr6:106564000-106564600	Enhancers	NHDF-Ad	bronchial
48	chr6:106564000-106564800	Enhancers	Brain Angular Gyrus	brain
49	chr6:106564000-106564800	Enhancers	Fetal Stomach	stomach
50	chr6:106564000-106566600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links