Variant report

Variant	rs7979755
Chromosome Location	chr12:31789673-31789674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31477087..31479390-chr12:31788128..31791122,2	K562	blood:
2	chr12:31555750..31556431-chr12:31789633..31790210,2	MCF-7	breast:
3	chr12:31555778..31556722-chr12:31789039..31790321,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METTL20-3	chr12:31789304-31789914	NONHSAT027565

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction
ENSG00000177340	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11051507	0.81[TSI][hapmap]
rs11051508	0.81[TSI][hapmap]
rs12826630	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12827275	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2374165	0.81[TSI][hapmap]
rs34229621	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844104	0.83[EUR][1000 genomes]
rs498080	0.90[ASN][1000 genomes]
rs6487998	0.81[TSI][hapmap]
rs73088360	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967518	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7975536	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7979755	PTHLH	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31783400-31789800	Weak transcription	Placenta	Placenta
2	chr12:31783400-31803000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:31783400-31803000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:31783600-31792600	Weak transcription	Pancreas	Pancrea
5	chr12:31784600-31794000	Weak transcription	Ovary	ovary
6	chr12:31788000-31793200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:31789000-31791000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:31789200-31789800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:31789200-31789800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:31789200-31789800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr12:31789200-31789800	Active TSS	Rectal Smooth Muscle	rectum
12	chr12:31789200-31789800	Active TSS	GM12878-XiMat	blood
13	chr12:31789200-31789800	Enhancers	Hela-S3	cervix
14	chr12:31789200-31790000	Enhancers	Duodenum Mucosa	Duodenum
15	chr12:31789200-31790200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:31789400-31789800	Active TSS	Primary B cells from cord blood	blood
17	chr12:31789400-31789800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:31789400-31789800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:31789400-31789800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:31789400-31789800	Flanking Active TSS	A549	lung
21	chr12:31789400-31790000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr12:31789600-31789800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr12:31789600-31789800	Enhancers	Adipose Nuclei	Adipose
24	chr12:31789600-31789800	Enhancers	K562	blood
25	chr12:31789600-31790800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr12:31789600-31803000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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