Variant report

Variant	rs183646
Chromosome Location	chr12:46273882-46273883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46120711..46122755-chr12:46271745..46274620,3	K562	blood:
2	chr12:46271607..46274125-chr12:46289637..46291918,2	K562	blood:
3	chr12:46121122..46123721-chr12:46273373..46275496,2	MCF-7	breast:
4	chr12:46197632..46200157-chr12:46272814..46274582,2	MCF-7	breast:
5	chr12:46273812..46279067-chr12:46282105..46286818,5	K562	blood:
6	chr12:46272488..46274410-chr12:46275573..46277238,2	K562	blood:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000270429	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10880841	0.94[CEU][hapmap];0.86[TSI][hapmap]
rs10880853	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs11183166	0.94[CEU][hapmap]
rs12423797	0.83[AFR][1000 genomes]
rs12426716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes]
rs1291625	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[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];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1366023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1427749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17712809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
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];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs2059405	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs2114844	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs2188119	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs247927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123	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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768660	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]
rs4768662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4768671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582578	0.94[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299892	0.92[ASN][1000 genomes]
rs7309711	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73097309	0.81[EUR][1000 genomes]
rs73097315	0.82[EUR][1000 genomes]
rs73097319	0.83[EUR][1000 genomes]
rs764192	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961085	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973329	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs975444	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv558782	chr12:46254995-46286683	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs183646	PDZRN4	cis	cerebellum	SCAN
rs183646	NELL2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46246000-46285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:46246600-46274800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:46246600-46285400	Weak transcription	NH-A	brain
5	chr12:46246600-46285600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:46246600-46286000	Weak transcription	HMEC	breast
7	chr12:46246800-46288000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:46248000-46275400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:46248000-46279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:46248000-46279600	Weak transcription	Gastric	stomach
11	chr12:46251800-46283400	Strong transcription	Fetal Thymus	thymus
12	chr12:46252400-46277400	Strong transcription	Dnd41	blood
13	chr12:46254800-46278600	Weak transcription	NHEK	skin
14	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:46262200-46278400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:46268000-46274600	Weak transcription	Lung	lung
17	chr12:46269000-46279400	Weak transcription	Pancreas	Pancrea
18	chr12:46269000-46287000	Weak transcription	Esophagus	oesophagus
19	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
20	chr12:46269200-46289000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:46269400-46274800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
23	chr12:46269600-46274200	Weak transcription	GM12878-XiMat	blood
24	chr12:46269600-46274600	Weak transcription	Fetal Brain Male	brain
25	chr12:46269600-46274600	Weak transcription	HepG2	liver
26	chr12:46269600-46278600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:46269600-46285600	Weak transcription	HSMM	muscle
28	chr12:46269600-46285600	Weak transcription	HSMMtube	muscle
29	chr12:46269600-46285800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:46269600-46287800	Weak transcription	Colonic Mucosa	Colon
31	chr12:46269800-46275000	Weak transcription	Adipose Nuclei	Adipose
32	chr12:46269800-46275200	Weak transcription	Placenta	Placenta
33	chr12:46269800-46276600	Weak transcription	Hela-S3	cervix
34	chr12:46269800-46279000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:46269800-46285800	Weak transcription	Fetal Kidney	kidney
36	chr12:46269800-46285800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:46269800-46285800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr12:46270000-46274400	Weak transcription	Primary B cells from cord blood	blood
40	chr12:46270000-46275000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:46270000-46279200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:46270000-46279200	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:46270000-46287200	Weak transcription	Osteobl	bone
44	chr12:46270200-46278400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:46270200-46279400	Weak transcription	Left Ventricle	heart
46	chr12:46270200-46285800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:46270400-46275600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:46270600-46279200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr12:46270800-46274400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:46270800-46274400	Weak transcription	Rectal Mucosa Donor 29	rectum

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