Variant report

Variant	rs4768659
Chromosome Location	chr12:46115349-46115350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45982849..45985395-chr12:46114233..46117039,2	K562	blood:
2	chr12:46102452..46106078-chr12:46112003..46116824,4	K562	blood:
3	chr12:46107312..46109855-chr12:46114820..46116430,3	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10880841	0.94[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs10880846	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880847	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880848	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880849	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880850	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10880851	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10880853	0.94[CEU][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183166	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11183173	0.91[EUR][1000 genomes]
rs11183178	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183179	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183180	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183181	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610813	0.90[EUR][1000 genomes]
rs11613663	0.90[EUR][1000 genomes]
rs12318735	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12320114	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12367059	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12423797	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12424874	0.90[EUR][1000 genomes]
rs12426716	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427001	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427272	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17712083	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17712809	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17774089	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17774927	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs183646	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2059405	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111963	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2160983	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2188119	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs2408436	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247927	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2897910	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35123	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs35124	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs3759404	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4512915	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4514487	0.84[EUR][1000 genomes]
rs4768660	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768662	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57267123	0.85[EUR][1000 genomes]
rs67790232	0.82[EUR][1000 genomes]
rs73095421	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73095422	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73095489	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73097309	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73097315	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73097319	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485654	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs875493	0.82[CHB][hapmap];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	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
rs4768659	NELL2	cis	cerebellum	SCAN
rs4768659	PDZRN4	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46097800-46118800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:46099600-46115600	Weak transcription	Ovary	ovary
3	chr12:46100600-46118800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:46101400-46115600	Weak transcription	Brain Substantia Nigra	brain
5	chr12:46105000-46116600	Weak transcription	Fetal Kidney	kidney
6	chr12:46106400-46115400	Weak transcription	GM12878-XiMat	blood
7	chr12:46106400-46115600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:46106400-46115600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:46107600-46118000	Weak transcription	NHEK	skin
10	chr12:46107600-46118200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:46107600-46118800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:46107600-46119000	Weak transcription	HSMM	muscle
13	chr12:46108400-46118600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:46108600-46115800	Weak transcription	Aorta	Aorta
15	chr12:46108800-46119000	Weak transcription	Fetal Stomach	stomach
16	chr12:46109000-46116800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:46109200-46115400	Weak transcription	Thymus	Thymus
18	chr12:46109400-46115600	Weak transcription	Esophagus	oesophagus
19	chr12:46110000-46116600	Weak transcription	Fetal Heart	heart
20	chr12:46110400-46119000	Weak transcription	Right Ventricle	heart
21	chr12:46110600-46119800	Weak transcription	Pancreas	Pancrea
22	chr12:46111000-46119000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:46111600-46117800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:46111600-46119200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:46111800-46117200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr12:46112000-46117200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:46112000-46118600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr12:46112200-46119000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:46112400-46117800	Weak transcription	Fetal Intestine Large	intestine
30	chr12:46112400-46118800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:46112600-46115600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:46112600-46117800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:46112800-46119000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:46113000-46115400	Genic enhancers	Dnd41	blood
35	chr12:46113000-46115600	Enhancers	Primary T cells from cord blood	blood
36	chr12:46113000-46116200	Enhancers	Psoas Muscle	Psoas
37	chr12:46113200-46115400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:46113200-46118000	Weak transcription	HepG2	liver
39	chr12:46113200-46118800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:46113400-46117400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:46113400-46118800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:46113400-46118800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:46113600-46115400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:46113600-46116400	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:46113600-46118600	Weak transcription	K562	blood
46	chr12:46113800-46116600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:46114000-46115400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:46114000-46115800	Strong transcription	Fetal Thymus	thymus
49	chr12:46114000-46116000	Weak transcription	Primary B cells from cord blood	blood
50	chr12:46114000-46118000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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