Variant report

Variant	rs7925137
Chromosome Location	chr11:47202946-47202947
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47196068..47203526-chr11:47288943..47293025,13	MCF-7	breast:
2	chr11:47201377..47203716-chr11:47267132..47269463,2	K562	blood:
3	chr11:47202119..47205492-chr11:47206060..47209673,5	K562	blood:
4	chr11:47202498..47205214-chr11:47434945..47437570,2	K562	blood:
5	chr11:47201513..47203398-chr11:47279251..47281417,2	MCF-7	breast:
6	chr11:47201336..47204009-chr11:47374499..47376871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165912	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11039106	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867972	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740691	0.95[GIH][hapmap]
rs3740694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7130989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940473	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948786	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv897324	chr11:47193566-47212032	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7925137	ARFGAP2	cis	cerebellum	SCAN
rs7925137	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47197000-47207600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr11:47198800-47206400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47199400-47204000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
4	chr11:47199600-47203200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:47199600-47204200	Weak transcription	Thymus	Thymus
6	chr11:47199600-47204800	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr11:47199600-47205600	Weak transcription	NHLF	lung
8	chr11:47199600-47206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:47199600-47206600	Weak transcription	HUVEC	blood vessel
10	chr11:47199600-47206800	Weak transcription	Fetal Kidney	kidney
11	chr11:47199600-47207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:47199800-47203800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:47199800-47204800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:47199800-47204800	Strong transcription	Fetal Lung	lung
15	chr11:47199800-47205000	Weak transcription	Stomach Mucosa	stomach
16	chr11:47199800-47205200	Weak transcription	Fetal Thymus	thymus
17	chr11:47199800-47205600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:47199800-47205800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:47199800-47206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:47199800-47206200	Strong transcription	NHEK	skin
21	chr11:47199800-47206400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:47199800-47206400	Weak transcription	Osteobl	bone
23	chr11:47200000-47203800	Weak transcription	Psoas Muscle	Psoas
24	chr11:47200000-47203800	Weak transcription	Right Atrium	heart
25	chr11:47200000-47203800	Weak transcription	Spleen	Spleen
26	chr11:47200000-47204200	Weak transcription	HSMMtube	muscle
27	chr11:47200000-47205000	Weak transcription	NHDF-Ad	bronchial
28	chr11:47200000-47205600	Weak transcription	Colonic Mucosa	Colon
29	chr11:47200000-47205600	Strong transcription	Fetal Stomach	stomach
30	chr11:47200000-47205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:47200000-47205800	Weak transcription	Adipose Nuclei	Adipose
32	chr11:47200000-47205800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:47200000-47206000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:47200000-47206200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:47200000-47206600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:47200000-47206600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:47200000-47207200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:47200200-47203000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr11:47200200-47204400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:47200200-47204800	Strong transcription	Pancreas	Pancrea
41	chr11:47200200-47205600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:47200200-47206400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:47200200-47206800	Weak transcription	Dnd41	blood
44	chr11:47200400-47205000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:47200400-47207200	Weak transcription	K562	blood
46	chr11:47200600-47203200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:47201200-47203000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:47201200-47204000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:47201400-47205200	Strong transcription	Placenta	Placenta
50	chr11:47201600-47203800	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links