Variant report

Variant	rs12129768
Chromosome Location	chr1:84628655-84628656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12128677	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134236	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12139683	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12144770	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17535312	1.00[ASN][1000 genomes]
rs2684910	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661411	1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv546690	chr1:84562265-84655238	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv871731	chr1:84597396-84658591	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv997601	chr1:84609346-84672859	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1005225	chr1:84609871-84667950	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1002537	chr1:84611207-84658450	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv999772	chr1:84611207-84667218	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1013911	chr1:84619164-84667950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv871375	chr1:84622793-84678418	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12129768	LOC339524	cis	cerebellum	SCAN
rs12129768	MCOLN2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84610400-84633400	Weak transcription	Fetal Kidney	kidney
2	chr1:84611600-84629800	Weak transcription	Fetal Stomach	stomach
3	chr1:84612800-84628800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:84614000-84633800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:84614800-84629000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:84615800-84634800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:84616200-84635200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:84618800-84630400	Weak transcription	Primary B cells from cord blood	blood
9	chr1:84619000-84628800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:84619000-84628800	Weak transcription	Gastric	stomach
11	chr1:84619200-84630200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:84622000-84628800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:84622200-84630000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:84622400-84635800	Weak transcription	Small Intestine	intestine
15	chr1:84622600-84628800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:84623000-84629800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:84623000-84639200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:84623800-84630000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:84624000-84628800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:84624000-84629200	Weak transcription	Fetal Thymus	thymus
21	chr1:84624000-84651800	Weak transcription	Thymus	Thymus
22	chr1:84624200-84630800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:84624800-84633200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:84625200-84629600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:84625600-84629800	Weak transcription	Right Atrium	heart
26	chr1:84625600-84635600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:84625800-84628800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:84625800-84634000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:84626000-84628800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:84626000-84630000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:84626200-84628800	Weak transcription	Dnd41	blood
32	chr1:84626400-84630400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr1:84626600-84629000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:84626800-84628800	Weak transcription	Brain Anterior Caudate	brain
35	chr1:84627200-84631000	Weak transcription	HUVEC	blood vessel
36	chr1:84627600-84635400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:84627800-84629400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:84628200-84628800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:84628200-84628800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:84628200-84628800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:84628600-84628800	Active TSS	Primary T cells from cord blood	blood
42	chr1:84628600-84628800	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links