Variant report

Variant	rs4768925
Chromosome Location	chr12:51218323-51218324
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51218257..51221554-chr12:51475850..51478812,3	MCF-7	breast:
2	chr12:51157232..51159790-chr12:51217662..51220370,4	MCF-7	breast:
3	chr12:51216774..51221510-chr12:51379576..51384198,5	MCF-7	breast:
4	chr12:51218193..51220790-chr12:51416290..51419028,2	K562	blood:
5	chr12:51218097..51220673-chr12:51419291..51422139,4	MCF-7	breast:
6	chr12:51216775..51221102-chr12:51419333..51421670,3	K562	blood:
7	chr12:50793039..50794712-chr12:51216768..51219272,2	K562	blood:
8	chr12:51184951..51187491-chr12:51218198..51219760,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506294	0.84[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.88[MKK][hapmap]
rs10506295	0.81[CHB][hapmap]
rs10747587	0.84[ASW][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.92[MKK][hapmap]
rs10783382	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10783389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10876076	0.81[CHB][hapmap]
rs10876080	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10876081	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10876089	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10876090	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10876094	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10876095	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876097	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169515	0.81[CHB][hapmap]
rs11169532	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11169538	1.00[JPT][hapmap]
rs11169544	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11169552	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11169554	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11169560	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11169561	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12231309	0.81[CHB][hapmap]
rs12424860	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12809086	0.81[CHB][hapmap]
rs1344958	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3742064	0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs3809319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3825402	0.95[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs4026593	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4238108	0.81[CHB][hapmap]
rs4307773	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4768866	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs4768907	0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs4768914	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs4768917	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4768921	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4768922	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4768923	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768924	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768940	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73094900	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73096846	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs864899	0.82[CHB][hapmap]
rs876078	0.84[ASW][hapmap];0.93[GIH][hapmap];0.92[MKK][hapmap]
rs952318	0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3527700	chr12:51215835-51219508	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3527701	chr12:51215835-51219508	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3496675	chr12:51216090-51218740	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3496686	chr12:51216340-51218681	Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3496697	chr12:51216340-51218681	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv15451	chr12:51216724-51218337	Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768925	AQP2	cis	parietal	SCAN
rs4768925	LASS5	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:51205000-51228200	Weak transcription	Gastric	stomach
3	chr12:51208000-51219000	Weak transcription	Stomach Mucosa	stomach
4	chr12:51208400-51218800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:51208400-51219000	Weak transcription	HSMMtube	muscle
6	chr12:51208400-51219000	Weak transcription	NHLF	lung
7	chr12:51208600-51219000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:51209800-51219000	Weak transcription	Fetal Kidney	kidney
9	chr12:51210200-51222000	Weak transcription	Esophagus	oesophagus
10	chr12:51210400-51219000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:51210600-51219000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:51210600-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:51210600-51223400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:51210800-51218800	Weak transcription	HMEC	breast
15	chr12:51210800-51218800	Weak transcription	NHEK	skin
16	chr12:51211000-51218800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:51211000-51218800	Weak transcription	Brain Anterior Caudate	brain
18	chr12:51211000-51218800	Weak transcription	Brain Substantia Nigra	brain
19	chr12:51211000-51218800	Weak transcription	K562	blood
20	chr12:51211000-51219000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:51211000-51222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:51211000-51222000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:51211800-51218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:51212200-51218800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:51212200-51218800	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:51212200-51219000	Weak transcription	Fetal Intestine Large	intestine
27	chr12:51212200-51219400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:51212200-51219400	Weak transcription	Aorta	Aorta
29	chr12:51212200-51219400	Weak transcription	Ovary	ovary
30	chr12:51212400-51218800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:51212400-51218800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:51212400-51219000	Weak transcription	A549	lung
33	chr12:51212400-51219600	Weak transcription	Fetal Lung	lung
34	chr12:51213000-51219000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:51213000-51219000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:51213200-51218800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:51213200-51218800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:51213200-51219000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:51213200-51219000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:51213200-51219000	Weak transcription	Thymus	Thymus
41	chr12:51213200-51219400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:51213200-51222200	Weak transcription	Fetal Muscle Leg	muscle
43	chr12:51213400-51218600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:51213400-51219400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:51213400-51221800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:51213400-51222600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:51213600-51218800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:51213600-51219000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:51213600-51219000	Weak transcription	Primary T cells from cord blood	blood
50	chr12:51213600-51219000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links