Variant report

Variant	rs1316787
Chromosome Location	chr12:122489101-122489102
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122487454..122491014-chr12:122493192..122496631,4	K562	blood:
2	chr12:122487767..122490399-chr12:122506061..122507561,2	K562	blood:
3	chr12:122487474..122489659-chr12:122490996..122492915,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10770189	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840645	0.84[ASN][1000 genomes]
rs11059094	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs11835818	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12230227	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812519	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1880030	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1976859	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280573	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280574	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28461580	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs28530689	0.80[EUR][1000 genomes]
rs28605425	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs28629903	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28652632	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs28691281	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28759327	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34047484	0.82[EUR][1000 genomes]
rs34123446	0.80[EUR][1000 genomes]
rs34532891	0.82[EUR][1000 genomes]
rs34739240	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34974633	0.82[EUR][1000 genomes]
rs35159488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35249105	0.82[EUR][1000 genomes]
rs35676267	0.80[EUR][1000 genomes]
rs35764187	0.82[EUR][1000 genomes]
rs36079122	0.80[EUR][1000 genomes]
rs61952902	0.82[EUR][1000 genomes]
rs61952904	0.81[EUR][1000 genomes]
rs7137049	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7299842	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1316787	CCDC92	cis	cerebellum	SCAN
rs1316787	FAM101A	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122461600-122492400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:122462000-122492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:122462400-122490400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:122462400-122492200	Weak transcription	Stomach Mucosa	stomach
5	chr12:122462400-122500000	Weak transcription	Hela-S3	cervix
6	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:122466800-122490200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:122467800-122500000	Strong transcription	Thymus	Thymus
9	chr12:122467800-122500200	Strong transcription	Dnd41	blood
10	chr12:122468000-122489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:122468200-122492800	Weak transcription	NHDF-Ad	bronchial
12	chr12:122470000-122492400	Strong transcription	Fetal Thymus	thymus
13	chr12:122470000-122492400	Weak transcription	K562	blood
14	chr12:122470600-122489800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:122472000-122507200	Weak transcription	Fetal Brain Male	brain
16	chr12:122472400-122489600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:122472800-122489600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr12:122473000-122489600	Strong transcription	Fetal Brain Female	brain
19	chr12:122473600-122492800	Weak transcription	Esophagus	oesophagus
20	chr12:122474000-122496800	Weak transcription	HMEC	breast
21	chr12:122474400-122492200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:122474400-122496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:122474400-122500600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:122474600-122492400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:122475200-122501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:122477800-122489600	Strong transcription	Brain Germinal Matrix	brain
27	chr12:122479200-122493200	Weak transcription	Gastric	stomach
28	chr12:122479400-122489800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:122479400-122492400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:122479400-122500600	Weak transcription	Small Intestine	intestine
31	chr12:122479800-122491600	Strong transcription	Fetal Intestine Small	intestine
32	chr12:122481000-122489400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:122482200-122491200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:122482600-122492200	Weak transcription	Placenta	Placenta
35	chr12:122482800-122492400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:122483400-122490400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:122483600-122492800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:122483600-122500200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:122483800-122492800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:122484400-122490200	Weak transcription	Brain Substantia Nigra	brain
41	chr12:122484400-122492600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:122484600-122492200	Weak transcription	Fetal Lung	lung
43	chr12:122484600-122492400	Weak transcription	Colonic Mucosa	Colon
44	chr12:122484600-122492400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:122484600-122493000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:122484800-122492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:122484800-122492600	Weak transcription	NHEK	skin
48	chr12:122484800-122493000	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:122484800-122495200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:122485000-122492800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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