Variant report

Variant	rs3890556
Chromosome Location	chr6:106555991-106555992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106543623..106549882-chr6:106552616..106559116,8	K562	blood:
2	chr6:106555778..106558773-chr6:106588143..106590176,2	K562	blood:
3	chr6:106554917..106557278-chr6:106588143..106590911,3	K562	blood:

Variant related genes	Relation type
ENSG00000057657	Chromatin interaction
ENSG00000269919	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12663005	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17558727	1.00[AMR][1000 genomes]
rs17558797	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2185379	0.96[EUR][1000 genomes]
rs6913893	0.81[AMR][1000 genomes]
rs9373830	0.85[AMR][1000 genomes]
rs9384600	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9386511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9398059	0.85[AMR][1000 genomes]
rs9398063	1.00[AMR][1000 genomes]
rs9398065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9398066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106546600-106559000	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:106546800-106560200	Weak transcription	HSMM	muscle
3	chr6:106546800-106567000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:106547200-106562600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:106547400-106557200	Strong transcription	Fetal Intestine Large	intestine
6	chr6:106547400-106558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:106547400-106560200	Weak transcription	NH-A	brain
8	chr6:106547600-106556400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:106548000-106556600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:106548400-106561800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:106550800-106556400	Strong transcription	Fetal Intestine Small	intestine
12	chr6:106551600-106559200	Weak transcription	Brain Anterior Caudate	brain
13	chr6:106551600-106560400	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:106551600-106563800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:106551800-106556200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:106551800-106556400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:106551800-106556400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:106551800-106556400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:106551800-106557800	Weak transcription	Stomach Mucosa	stomach
20	chr6:106551800-106563000	Weak transcription	HSMMtube	muscle
21	chr6:106551800-106564000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:106551800-106564000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:106552000-106556200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr6:106552000-106557200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:106552000-106557800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:106552000-106558600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:106552000-106559200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:106552000-106559400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:106552200-106556800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:106552400-106556000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:106552400-106557800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:106552600-106556400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr6:106552600-106556600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:106552600-106556800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:106552600-106557200	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr6:106552600-106558600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:106552800-106556000	Strong transcription	Colonic Mucosa	Colon
38	chr6:106553000-106556000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr6:106553400-106558200	Weak transcription	Pancreas	Pancrea
40	chr6:106553600-106584000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:106553800-106556400	Strong transcription	Osteobl	bone
42	chr6:106553800-106556600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:106554000-106556400	Strong transcription	Lung	lung
44	chr6:106554000-106556800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr6:106554400-106556200	Strong transcription	Placenta	Placenta
46	chr6:106554400-106556400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr6:106554600-106566800	Weak transcription	Hela-S3	cervix
48	chr6:106554800-106558600	Weak transcription	Small Intestine	intestine
49	chr6:106554800-106564000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:106555000-106557200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links