Variant report

Variant	rs12901353
Chromosome Location	chr15:49479478-49479479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49470753..49473107-chr15:49477879..49480069,2	K562	blood:
2	chr15:49471607..49473111-chr15:49477879..49479723,2	K562	blood:
3	chr15:49463826..49467662-chr15:49477786..49482554,6	K562	blood:

Variant related genes	Relation type
ENSG00000259545	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10519224	1.00[AFR][1000 genomes]
rs10519225	1.00[AFR][1000 genomes]
rs11853969	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854039	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854184	0.90[LWK][hapmap]
rs11854557	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11855798	1.00[AFR][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11857773	0.83[ASN][1000 genomes]
rs11858814	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591300	0.96[AFR][1000 genomes]
rs12592508	0.88[CEU][hapmap]
rs12899422	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900819	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12900838	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12901929	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12902096	0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12902271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12905094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905203	0.81[CEU][hapmap]
rs12905477	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914876	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17393761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17435932	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17472989	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961393	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2413926	0.80[CEU][hapmap]
rs34562714	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748066	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023246	1.00[AFR][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4775794	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4775806	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62009762	0.85[ASN][1000 genomes]
rs62009834	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71467664	0.81[ASN][1000 genomes]
rs7164309	0.81[CEU][hapmap]
rs7180168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8043493	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672848	0.81[AFR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12901353	LCMT2	cis	parietal	SCAN
rs12901353	SPATA5L1	cis	parietal	SCAN
rs12901353	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463000-49479600	Weak transcription	Left Ventricle	heart
2	chr15:49463200-49479600	Weak transcription	Right Ventricle	heart
3	chr15:49463200-49479800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:49463200-49508200	Weak transcription	Ovary	ovary
5	chr15:49463400-49480000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:49463600-49479600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:49463600-49494400	Weak transcription	Fetal Thymus	thymus
8	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:49463600-49527800	Weak transcription	HSMM	muscle
10	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
11	chr15:49464000-49482800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:49464000-49491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:49464200-49481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:49464400-49493800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:49464400-49493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:49464400-49500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:49464800-49479600	Weak transcription	NHLF	lung
18	chr15:49464800-49481800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:49465200-49494000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:49465400-49479600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:49465400-49508200	Weak transcription	Hela-S3	cervix
22	chr15:49466800-49482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:49467600-49494200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:49467800-49479600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:49468400-49494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:49468600-49479600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:49470200-49480000	Weak transcription	Fetal Intestine Small	intestine
28	chr15:49472800-49497200	Weak transcription	Brain Anterior Caudate	brain
29	chr15:49473000-49481600	Weak transcription	K562	blood
30	chr15:49473000-49483400	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:49473600-49479800	Weak transcription	Lung	lung
32	chr15:49473600-49483200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:49474800-49490200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:49476800-49483400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:49478000-49482800	Weak transcription	GM12878-XiMat	blood
36	chr15:49478000-49493800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:49478000-49494400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:49478000-49496000	Weak transcription	Primary T cells from cord blood	blood
39	chr15:49478200-49479600	Weak transcription	Gastric	stomach
40	chr15:49478400-49482800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:49478400-49497400	Weak transcription	Primary B cells from cord blood	blood
42	chr15:49478600-49481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:49479200-49479600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:49479200-49480000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:49479400-49479800	Enhancers	Stomach Mucosa	stomach
46	chr15:49479400-49480200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:49479400-49480600	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr15:49479400-49480600	Enhancers	Osteobl	bone
49	chr15:49479400-49480800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:49479400-49481400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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