Variant report

Variant	rs12136973
Chromosome Location	chr1:175140319-175140320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175139577..175141304-chr1:175158200..175161170,2	K562	blood:
2	chr1:175065484..175067807-chr1:175139999..175142698,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1008459	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs12563833	0.80[CEU][hapmap]
rs2272785	1.00[ASW][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs2861158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766686	0.86[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs3766690	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766691	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv528874	chr1:175140319-175151183	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12136973	KIAA0040	cis	lymphoblastoid	seeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
2	chr1:175126800-175141800	Strong transcription	Primary B cells from cord blood	blood
3	chr1:175126800-175148800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:175127000-175148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:175127200-175147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:175127400-175144200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:175127400-175149400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:175127600-175140600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:175129200-175159600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:175130200-175152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:175130400-175143400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:175135000-175152600	Weak transcription	Aorta	Aorta
13	chr1:175135000-175158400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:175135800-175146000	Weak transcription	Colonic Mucosa	Colon
15	chr1:175135800-175146000	Weak transcription	Fetal Intestine Large	intestine
16	chr1:175136000-175141800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:175136000-175142200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:175136000-175145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:175136000-175145400	Weak transcription	Ovary	ovary
20	chr1:175136000-175151600	Weak transcription	Fetal Stomach	stomach
21	chr1:175136000-175157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:175136200-175141800	Weak transcription	Psoas Muscle	Psoas
23	chr1:175136200-175145000	Weak transcription	Fetal Thymus	thymus
24	chr1:175136200-175146800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:175136600-175145200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:175137400-175145400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:175137600-175140600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:175137800-175140600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:175137800-175140800	Genic enhancers	Lung	lung
30	chr1:175137800-175140800	Enhancers	Small Intestine	intestine
31	chr1:175138000-175140400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:175138000-175140400	Genic enhancers	NHEK	skin
33	chr1:175138000-175143200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:175138000-175148000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:175138400-175140400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:175138400-175140400	Enhancers	Duodenum Mucosa	Duodenum
37	chr1:175138400-175145200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:175138600-175140400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr1:175138600-175141400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:175138800-175141800	Weak transcription	GM12878-XiMat	blood
41	chr1:175139000-175140600	Enhancers	Gastric	stomach
42	chr1:175139000-175140800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr1:175139200-175140600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:175139200-175140600	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr1:175139200-175141200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:175139200-175141600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:175139200-175143400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:175139200-175145400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:175139400-175140600	Enhancers	Hela-S3	cervix
50	chr1:175139400-175142400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links