Variant report

Variant	rs9462488
Chromosome Location	chr6:39160829-39160830
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39159378..39160886-chr6:39162592..39164483,2	MCF-7	breast:
2	chr6:39152659..39161573-chr6:39191951..39198831,12	K562	blood:
3	chr6:39160517..39162848-chr6:39178719..39180360,2	MCF-7	breast:
4	chr6:39158722..39165685-chr6:39165726..39171665,10	K562	blood:
5	chr6:39160661..39163154-chr6:39237331..39239168,2	MCF-7	breast:
6	chr6:39155353..39158584-chr6:39158946..39166191,7	K562	blood:
7	chr6:39155493..39158185-chr6:39159701..39165340,4	K562	blood:
8	chr6:39159091..39165465-chr6:39185781..39190794,6	K562	blood:
9	chr6:39147161..39148825-chr6:39159496..39161252,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2395715	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs9462495	1.00[AFR][1000 genomes]
rs9462508	1.00[CEU][hapmap]
rs9462518	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs9462519	1.00[AFR][1000 genomes]
rs9462520	1.00[AFR][1000 genomes]
rs9462521	1.00[CEU][hapmap]
rs9471004	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9471005	1.00[AFR][1000 genomes]
rs9471011	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs9471017	1.00[AFR][1000 genomes]
rs9471026	1.00[AFR][1000 genomes]
rs9471037	1.00[AFR][1000 genomes]
rs9471047	1.00[AFR][1000 genomes]
rs9471049	1.00[AFR][1000 genomes]
rs9471052	1.00[AFR][1000 genomes]
rs9471053	1.00[AFR][1000 genomes]
rs9471056	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS 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 target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 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	chr6:39149000-39168000	Weak transcription	Fetal Kidney	kidney
2	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
3	chr6:39151000-39165200	Strong transcription	H9 Cell Line	embryonic stem cell
4	chr6:39151400-39162200	Weak transcription	Thymus	Thymus
5	chr6:39151600-39161000	Strong transcription	Fetal Stomach	stomach
6	chr6:39153200-39162000	Genic enhancers	Placenta	Placenta
7	chr6:39154200-39164200	Genic enhancers	Fetal Intestine Large	intestine
8	chr6:39154400-39162400	Weak transcription	Hela-S3	cervix
9	chr6:39154400-39164400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:39155400-39172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:39155600-39164000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:39155600-39166600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:39156200-39164200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:39156400-39177200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:39156600-39161000	Weak transcription	Fetal Lung	lung
16	chr6:39156600-39164200	Weak transcription	HSMMtube	muscle
17	chr6:39156600-39169600	Weak transcription	A549	lung
18	chr6:39156800-39165200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:39156800-39166000	Weak transcription	Small Intestine	intestine
20	chr6:39156800-39166200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:39156800-39171200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:39157000-39164800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:39157200-39161200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:39157200-39163800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:39157200-39163800	Genic enhancers	Duodenum Mucosa	Duodenum
27	chr6:39157200-39163800	Strong transcription	Gastric	stomach
28	chr6:39157400-39161400	Weak transcription	Adipose Nuclei	Adipose
29	chr6:39157400-39166800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:39157600-39161200	Strong transcription	Spleen	Spleen
31	chr6:39157600-39163800	Strong transcription	Ovary	ovary
32	chr6:39158000-39162600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:39158000-39163800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:39158000-39165000	Strong transcription	Fetal Thymus	thymus
35	chr6:39158200-39161000	Strong transcription	Esophagus	oesophagus
36	chr6:39158200-39162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:39158200-39163800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:39158200-39164400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr6:39158400-39161000	Strong transcription	Liver	Liver
40	chr6:39158400-39161200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:39158400-39163600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:39158400-39164600	Genic enhancers	Stomach Mucosa	stomach
43	chr6:39158600-39161400	Strong transcription	Pancreas	Pancrea
44	chr6:39158600-39162800	Strong transcription	Lung	lung
45	chr6:39158600-39163400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr6:39158600-39163800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:39158800-39161000	Strong transcription	Colonic Mucosa	Colon
48	chr6:39158800-39161200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:39158800-39163000	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:39159000-39163800	Strong transcription	Rectal Mucosa Donor 29	rectum

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