Variant report

Variant	rs3778448
Chromosome Location	chr6:39163201-39163202
allele	A/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39160875..39164831-chr6:39173251..39175892,4	K562	blood:
2	chr6:39159378..39160886-chr6:39162592..39164483,2	MCF-7	breast:
3	chr6:39162719..39164812-chr6:39191321..39194021,2	K562	blood:
4	chr6:39158722..39165685-chr6:39165726..39171665,10	K562	blood:
5	chr6:39155353..39158584-chr6:39158946..39166191,7	K562	blood:
6	chr6:39155493..39158185-chr6:39159701..39165340,4	K562	blood:
7	chr6:39162734..39164328-chr6:39181033..39182674,2	K562	blood:
8	chr6:39159091..39165465-chr6:39185781..39190794,6	K562	blood:
9	chr6:39162911..39167327-chr6:39168116..39172779,6	MCF-7	breast:
10	chr6:39161548..39165736-chr6:39172380..39175639,5	K562	blood:
11	chr6:39156644..39158244-chr6:39161894..39164372,2	MCF-7	breast:

No data

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2815095	0.82[JPT][hapmap]
rs2815116	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs733701	0.82[JPT][hapmap]
rs9394578	0.82[JPT][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3778448	CUL9	cis	parietal	SCAN
rs3778448	PIM1	cis	parietal	SCAN
rs3778448	RPL10A	cis	cerebellum	SCAN
rs3778448	LRFN2	cis	parietal	SCAN

Chromatin state (count:66 , 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	chr6:39154200-39164200	Genic enhancers	Fetal Intestine Large	intestine
5	chr6:39154400-39164400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:39155400-39172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:39155600-39164000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:39155600-39166600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:39156200-39164200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:39156400-39177200	Weak transcription	Primary T cells from cord blood	blood
11	chr6:39156600-39164200	Weak transcription	HSMMtube	muscle
12	chr6:39156600-39169600	Weak transcription	A549	lung
13	chr6:39156800-39165200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:39156800-39166000	Weak transcription	Small Intestine	intestine
15	chr6:39156800-39166200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:39156800-39171200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:39157000-39164800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:39157200-39163800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:39157200-39163800	Genic enhancers	Duodenum Mucosa	Duodenum
21	chr6:39157200-39163800	Strong transcription	Gastric	stomach
22	chr6:39157400-39166800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:39157600-39163800	Strong transcription	Ovary	ovary
24	chr6:39158000-39163800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:39158000-39165000	Strong transcription	Fetal Thymus	thymus
26	chr6:39158200-39163800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:39158200-39164400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr6:39158400-39163600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:39158400-39164600	Genic enhancers	Stomach Mucosa	stomach
30	chr6:39158600-39163400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:39158600-39163800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:39159000-39163800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr6:39160600-39163600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr6:39161000-39165400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:39161200-39163400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:39161200-39164600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:39161400-39163800	Genic enhancers	Pancreas	Pancrea
38	chr6:39161600-39163800	Strong transcription	Esophagus	oesophagus
39	chr6:39161600-39164200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:39161600-39164400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:39161800-39163800	Strong transcription	Colonic Mucosa	Colon
42	chr6:39161800-39164000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:39161800-39164200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:39161800-39168600	Genic enhancers	K562	blood
45	chr6:39162000-39164200	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:39162000-39164200	Strong transcription	Placenta	Placenta
47	chr6:39162000-39164400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:39162200-39163600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:39162200-39163600	Strong transcription	Spleen	Spleen
50	chr6:39162200-39163800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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