Variant report

Variant	rs6477002
Chromosome Location	chr9:5838816-5838817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5830293..5833393-chr9:5836057..5839242,4	K562	blood:
2	chr9:5838320..5841107-chr9:5866547..5869554,3	MCF-7	breast:
3	chr9:5805477..5807590-chr9:5838086..5840721,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10975340	1.00[EUR][1000 genomes]
rs1141025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260130	1.00[EUR][1000 genomes]
rs1260132	1.00[EUR][1000 genomes]
rs1260134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260135	1.00[EUR][1000 genomes]
rs1745887	1.00[EUR][1000 genomes]
rs1776008	1.00[EUR][1000 genomes]
rs2476262	1.00[EUR][1000 genomes]
rs2760408	1.00[EUR][1000 genomes]
rs2760409	1.00[EUR][1000 genomes]
rs2760410	1.00[EUR][1000 genomes]
rs2797512	1.00[EUR][1000 genomes]
rs2797514	1.00[EUR][1000 genomes]
rs2797516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797517	0.83[AMR][1000 genomes]
rs2797519	1.00[EUR][1000 genomes]
rs58370080	1.00[EUR][1000 genomes]
rs6477001	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7037680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042539	1.00[AMR][1000 genomes]
rs7046793	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73377834	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	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
3	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1016365	chr9:5828435-5850834	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5833400-5839000	Weak transcription	Esophagus	oesophagus
2	chr9:5833400-5858000	Weak transcription	Aorta	Aorta
3	chr9:5833600-5843400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:5833800-5839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:5834000-5839000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:5834000-5839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:5834000-5839000	Weak transcription	Fetal Intestine Large	intestine
8	chr9:5834000-5839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:5834000-5839000	Weak transcription	Stomach Mucosa	stomach
10	chr9:5834000-5839000	Weak transcription	NHEK	skin
11	chr9:5834000-5839200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr9:5834000-5839200	Weak transcription	GM12878-XiMat	blood
13	chr9:5834000-5839400	Weak transcription	Right Atrium	heart
14	chr9:5834000-5842000	Weak transcription	Fetal Brain Male	brain
15	chr9:5834000-5843000	Weak transcription	Small Intestine	intestine
16	chr9:5834000-5843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:5834000-5843400	Weak transcription	Colonic Mucosa	Colon
18	chr9:5834200-5839000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:5834200-5839000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:5834200-5839000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:5834200-5839000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:5834200-5839000	Weak transcription	Fetal Intestine Small	intestine
23	chr9:5834200-5839200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:5834200-5839200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:5834200-5839400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr9:5834200-5839400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr9:5834200-5839400	Weak transcription	Placenta	Placenta
28	chr9:5834200-5839400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:5834200-5839600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:5834200-5839600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:5834200-5839600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:5834200-5839600	Weak transcription	Right Ventricle	heart
33	chr9:5834200-5840800	Weak transcription	Fetal Kidney	kidney
34	chr9:5834200-5841000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:5834200-5841200	Weak transcription	Primary T cells from cord blood	blood
36	chr9:5834200-5841400	Weak transcription	Brain Hippocampus Middle	brain
37	chr9:5834200-5843000	Weak transcription	Fetal Lung	lung
38	chr9:5834200-5843800	Weak transcription	Spleen	Spleen
39	chr9:5834200-5844200	Weak transcription	Brain Substantia Nigra	brain
40	chr9:5834200-5855200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:5834200-5858200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:5834200-5858600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:5834400-5839000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr9:5834400-5843000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr9:5834400-5886000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr9:5834600-5839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:5834800-5839000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:5834800-5840400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:5835000-5839000	Weak transcription	Psoas Muscle	Psoas
50	chr9:5835000-5843200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links