Variant report

Variant	rs12470805
Chromosome Location	chr2:73162541-73162542
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:73113562..73116065-chr2:73161529..73164202,2	K562	blood:
2	chr2:73149221..73153083-chr2:73158827..73162674,4	MCF-7	breast:
3	chr2:73119772..73121378-chr2:73161774..73162754,8	K562	blood:
4	chr2:73119580..73120121-chr2:73162208..73162742,2	MCF-7	breast:
5	chr2:73162249..73166255-chr2:73168252..73172179,4	MCF-7	breast:
6	chr2:73089395..73090340-chr2:73161832..73162679,3	K562	blood:
7	chr2:73119149..73121443-chr2:73161355..73163899,24	MCF-7	breast:
8	chr2:73114739..73115657-chr2:73162083..73162771,2	MCF-7	breast:
9	chr2:73114519..73115299-chr2:73161801..73162747,2	K562	blood:
10	chr2:73154403..73156745-chr2:73162341..73165045,2	K562	blood:
11	chr2:73120289..73121434-chr2:73162133..73162762,4	MCF-7	breast:
12	chr2:73119837..73121902-chr2:73162197..73164658,2	MCF-7	breast:
13	chr2:73121732..73122347-chr2:73162003..73162549,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116096	Chromatin interaction
ENSG00000135638	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2077586	0.93[CEU][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs6709269	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv874266	chr2:73137991-73220138	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12470805	NAGK	cis	parietal	SCAN
rs12470805	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73157000-73163200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:73159400-73162600	Weak transcription	Fetal Brain Male	brain
3	chr2:73159400-73163400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:73159800-73169600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:73159800-73170600	Weak transcription	Aorta	Aorta
6	chr2:73160000-73166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:73160200-73163000	Strong transcription	Fetal Brain Female	brain
8	chr2:73160200-73163400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:73160200-73164200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:73161200-73162800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:73161200-73162800	Enhancers	HMEC	breast
12	chr2:73161400-73162800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:73161400-73162800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:73161400-73210200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:73161600-73162600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:73161800-73167200	Weak transcription	Spleen	Spleen
17	chr2:73162000-73162600	Enhancers	HepG2	liver
18	chr2:73162000-73167400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:73162200-73162600	Enhancers	Esophagus	oesophagus
20	chr2:73162400-73162600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
21	chr2:73162400-73162600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr2:73162400-73162600	Enhancers	NHEK	skin
23	chr2:73162400-73164800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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