Variant report

Variant	rs4768660
Chromosome Location	chr12:46136636-46136637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46134765..46138233-chr12:46138934..46141433,3	MCF-7	breast:
2	chr12:46135733..46138197-chr12:46140169..46142459,2	K562	blood:
3	chr12:46131503..46133931-chr12:46134942..46137165,2	MCF-7	breast:
4	chr12:46134325..46137231-chr12:46148233..46149975,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10880841	0.94[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10880846	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880847	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880848	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880849	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880850	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880851	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880853	0.94[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183166	0.94[CEU][hapmap]
rs11183173	0.86[EUR][1000 genomes]
rs11183178	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183179	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183180	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183181	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610813	0.85[EUR][1000 genomes]
rs11613663	0.85[EUR][1000 genomes]
rs12318735	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12320114	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367059	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12423797	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12424874	0.84[EUR][1000 genomes]
rs12426716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427001	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427272	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1291628	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs17712083	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17712809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17774089	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17774927	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs183646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2059405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111963	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2160983	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188119	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap]
rs2408436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2897910	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs35124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs3759404	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4512915	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768659	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6582578	0.94[CEU][hapmap]
rs73095421	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73095422	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73095489	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7309711	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap]
rs73097309	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73097315	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73097319	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485654	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs975444	0.84[EUR][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	nsv899052	chr12:46068394-46175469	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv899053	chr12:46100053-46141372	Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4768660	NELL2	cis	cerebellum	SCAN
rs4768660	PDZRN4	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46125000-46161200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:46125200-46140000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:46125200-46146400	Weak transcription	Left Ventricle	heart
4	chr12:46125200-46156000	Weak transcription	Small Intestine	intestine
5	chr12:46125400-46137600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:46125400-46142400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:46125400-46152200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:46126400-46142000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:46126400-46146000	Weak transcription	Right Ventricle	heart
10	chr12:46126400-46149600	Weak transcription	Right Atrium	heart
11	chr12:46126400-46161200	Weak transcription	Aorta	Aorta
12	chr12:46127200-46137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:46127200-46141800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:46127200-46141800	Weak transcription	NHDF-Ad	bronchial
15	chr12:46127200-46142800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:46127200-46142800	Weak transcription	Thymus	Thymus
17	chr12:46127200-46143400	Weak transcription	HSMMtube	muscle
18	chr12:46127200-46147600	Weak transcription	Colonic Mucosa	Colon
19	chr12:46127200-46150400	Weak transcription	NHLF	lung
20	chr12:46127200-46161200	Weak transcription	HMEC	breast
21	chr12:46127400-46144400	Weak transcription	NH-A	brain
22	chr12:46127400-46147600	Weak transcription	Fetal Heart	heart
23	chr12:46127400-46153600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:46127400-46154800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:46127400-46156000	Weak transcription	Adipose Nuclei	Adipose
26	chr12:46127600-46141600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:46127800-46149000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:46128000-46148000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:46128200-46164600	Weak transcription	Esophagus	oesophagus
30	chr12:46129200-46156600	Weak transcription	HepG2	liver
31	chr12:46129400-46156000	Weak transcription	Brain Angular Gyrus	brain
32	chr12:46129600-46137400	Weak transcription	Primary T cells from cord blood	blood
33	chr12:46129600-46144800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:46129600-46145400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:46130000-46137000	Weak transcription	Ovary	ovary
36	chr12:46130000-46147800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:46130400-46137000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:46130400-46147600	Weak transcription	Osteobl	bone
39	chr12:46131200-46136800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:46131200-46142800	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:46131200-46149200	Weak transcription	Placenta	Placenta
42	chr12:46131200-46149800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:46131200-46160800	Weak transcription	NHEK	skin
44	chr12:46131400-46138400	Weak transcription	Liver	Liver
45	chr12:46131400-46145000	Weak transcription	Gastric	stomach
46	chr12:46131400-46145200	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:46131400-46156200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:46131600-46147000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:46131600-46150600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:46131800-46140400	Weak transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links