Variant report

Variant	rs2855709
Chromosome Location	chr12:12013985-12013986
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11990610..11993968-chr12:12013101..12016369,3	K562	blood:
2	chr12:11990610..11993601-chr12:12013404..12016369,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17819115	0.91[CHB][hapmap]
rs2238121	0.81[GIH][hapmap];0.85[TSI][hapmap]
rs2238122	0.85[TSI][hapmap]
rs2238123	0.87[ASN][1000 genomes]
rs2238124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2238129	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2416944	0.89[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2710266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2710269	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2723803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2723804	0.85[TSI][hapmap]
rs2855707	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.98[ASN][1000 genomes]
rs6488463	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs928936	0.91[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832331	chr12:11925095-12114451	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv516796	chr12:12013985-12027745	Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2855709	M6PR	cis	parietal	SCAN
rs2855709	TAS2R20	cis	parietal	SCAN
rs2855709	TAS2R19	cis	parietal	SCAN
rs2855709	PRB3	cis	cerebellum	SCAN
rs2855709	ARHGDIB	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11980800-12022600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:11985800-12014800	Weak transcription	Fetal Brain Female	brain
3	chr12:11987600-12038000	Weak transcription	Hela-S3	cervix
4	chr12:11989400-12023000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:11992600-12014600	Weak transcription	NHEK	skin
6	chr12:11992600-12015600	Weak transcription	NHLF	lung
7	chr12:11992600-12015800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:11993000-12019000	Weak transcription	A549	lung
9	chr12:11993600-12014000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:11995600-12014000	Weak transcription	Psoas Muscle	Psoas
11	chr12:11996400-12022600	Weak transcription	HSMM	muscle
12	chr12:12004600-12016600	Weak transcription	Ovary	ovary
13	chr12:12005000-12022400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:12006200-12014800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:12006200-12015200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:12006400-12014000	Strong transcription	Osteobl	bone
17	chr12:12006800-12015600	Weak transcription	NHDF-Ad	bronchial
18	chr12:12008800-12018600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:12009000-12018800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:12009400-12017000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:12009400-12017800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:12009400-12030800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:12009600-12014000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:12009600-12014200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:12009600-12014200	Strong transcription	Thymus	Thymus
26	chr12:12009600-12014200	Strong transcription	GM12878-XiMat	blood
27	chr12:12009600-12014400	Weak transcription	Pancreas	Pancrea
28	chr12:12009600-12014600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:12009600-12014600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:12009600-12015200	Weak transcription	Small Intestine	intestine
31	chr12:12009600-12016400	Weak transcription	Colonic Mucosa	Colon
32	chr12:12009600-12019400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:12009800-12014400	Strong transcription	NH-A	brain
34	chr12:12010000-12014200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:12010200-12014000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:12010200-12014200	Weak transcription	Stomach Mucosa	stomach
37	chr12:12010200-12014400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:12010200-12014600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:12010400-12014200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:12010400-12015400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:12010400-12015800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr12:12010400-12016200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:12010400-12019200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:12010600-12015400	Weak transcription	Brain Anterior Caudate	brain
45	chr12:12010600-12015400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:12010600-12015400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:12010600-12015600	Weak transcription	HSMMtube	muscle
48	chr12:12010600-12019000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:12010800-12014200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:12010800-12015000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links