Variant report

Variant	rs6413453
Chromosome Location	chr1:161192316-161192317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:161191737-161192764	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:161187638-161194598	HepG2	liver:	n/a	n/a
3	MYBL2	chr1:161191656-161194634	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:161191743-161194547	HepG2	liver:	n/a	n/a
5	HEY1	chr1:161191669-161194540	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:161187501-161194535	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:161187261-161194848	HepG2	liver:	n/a	n/a
8	MBD4	chr1:161191635-161194538	HepG2	liver:	n/a	n/a
9	HEY1	chr1:161187602-161194631	HepG2	liver:	n/a	n/a
10	MYBL2	chr1:161192315-161194692	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:161192039-161193639	HepG2	liver:	n/a	n/a
12	NR2F2	chr1:161191611-161194624	HepG2	liver:	n/a	n/a
13	REST	chr1:161192061-161192355	HepG2	liver:	n/a	n/a
14	MBD4	chr1:161191636-161194471	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:161191482-161194479	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161191256..161193783-chr1:161281655..161284632,2	K562	blood:
2	chr1:161191860..161194631-chr1:161195444..161197295,2	MCF-7	breast:
3	chr1:161144654..161146766-chr1:161192298..161194395,2	MCF-7	breast:
4	chr1:161179772..161182627-chr1:161189790..161192489,3	MCF-7	breast:
5	chr1:161192147..161195116-chr1:161197570..161199818,2	MCF-7	breast:
6	chr1:161173950..161176366-chr1:161191214..161193773,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR5187	TF binding region
TOMM40L	TF binding region
ENSG00000158882	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000263548	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11584174	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs12077004	1.00[ASW][hapmap]
rs12116949	1.00[LWK][hapmap]
rs12721035	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs12721036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832733	1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap]
rs3402	1.00[ASW][hapmap]
rs4077629	1.00[YRI][hapmap]
rs4656998	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs4656999	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6686001	0.82[JPT][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6413453	NDUFS2	cis	cerebellum	SCAN
rs6413453	YY1AP1	cis	cerebellum	SCAN
rs6413453	DCAF8	cis	cerebellum	SCAN
rs6413453	SLAMF8	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161172800-161193600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:161182400-161193800	Weak transcription	Small Intestine	intestine
3	chr1:161184400-161195000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:161184400-161195000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:161184400-161195000	Weak transcription	NHEK	skin
6	chr1:161184600-161195000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:161184600-161195000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:161184600-161195000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:161184600-161195800	Weak transcription	Aorta	Aorta
10	chr1:161184600-161195800	Weak transcription	Esophagus	oesophagus
11	chr1:161185000-161194800	Weak transcription	Dnd41	blood
12	chr1:161185000-161195000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:161185200-161195000	Weak transcription	A549	lung
14	chr1:161185200-161195200	Weak transcription	Thymus	Thymus
15	chr1:161185400-161195200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:161185400-161195200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:161185400-161195200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:161185600-161195000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:161185600-161195200	Weak transcription	HMEC	breast
20	chr1:161185800-161192400	Weak transcription	Fetal Stomach	stomach
21	chr1:161185800-161195000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:161185800-161195800	Enhancers	Fetal Intestine Large	intestine
23	chr1:161186000-161194000	Weak transcription	Gastric	stomach
24	chr1:161186000-161195200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:161186600-161194000	Weak transcription	Stomach Mucosa	stomach
26	chr1:161186800-161194800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:161186800-161195000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:161187000-161195000	Weak transcription	Fetal Lung	lung
29	chr1:161187400-161195800	Weak transcription	Lung	lung
30	chr1:161187600-161194200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:161187600-161195200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:161187800-161195000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:161187800-161195000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:161187800-161195000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:161188200-161195000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:161188200-161195000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:161188400-161192800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr1:161188400-161195000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:161188400-161195000	Weak transcription	Adipose Nuclei	Adipose
40	chr1:161188600-161195000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:161189000-161195200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:161189400-161193000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:161189600-161195000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:161189800-161195000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:161190000-161195000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:161190000-161195000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:161190000-161195000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:161190000-161195200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:161190200-161194800	Weak transcription	Primary T cells from cord blood	blood
50	chr1:161190200-161195000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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