Variant report

Variant	rs12914501
Chromosome Location	chr15:40868469-40868470
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40867638..40870164-chr15:40881425..40883040,2	K562	blood:
2	chr15:40867311..40870142-chr15:40875469..40877107,2	K562	blood:
3	chr15:40866258..40868658-chr15:40873477..40876647,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 27 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1051482	1.00[CEU][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes]
rs10851396	0.96[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11070279	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070280	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852479	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855517	0.83[EUR][1000 genomes]
rs11857247	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12148185	1.00[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12899408	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906755	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs12907448	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12907984	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12908114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908443	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12908867	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12915563	0.92[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12916323	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1453183	1.00[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17746659	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17747399	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2123534	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2289219	0.83[CEU][hapmap]
rs2304583	0.92[CEU][hapmap]
rs2412545	0.92[CEU][hapmap]
rs28798094	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3213999	0.84[CEU][hapmap]
rs34303240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34750756	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35884042	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36094699	0.84[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803353	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4457966	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5030783	0.92[CEU][hapmap]
rs55954396	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56384845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61048252	0.85[EUR][1000 genomes]
rs62018046	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62018048	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62018051	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62019866	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62019883	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62019934	0.83[EUR][1000 genomes]
rs7162749	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164385	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7165054	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181909	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72733469	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs731640	0.80[CEU][hapmap]
rs733299	0.83[CEU][hapmap]
rs8025458	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028910	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8036938	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8038396	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042733	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9806410	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs999197	0.96[CEU][hapmap]

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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:27)

SNP	Gene	Cis/trans	Tissue	Source
rs12914501	RP11-111A22.1	cis	lung	GTEx
rs12914501	C15orf57	cis	Nerve Tibial	GTEx
rs12914501	C15orf57	cis	Stomach	GTEx
rs12914501	MGC20481	cis	multi-tissue	Pritchard
rs12914501	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs12914501	C15orf57	cis	Muscle Skeletal	GTEx
rs12914501	C15orf57	cis	Esophagus Muscularis	GTEx
rs12914501	CCDC32	cis	lesional skin	skin_eQTL
rs12914501	ZFYVE19	cis	multi-tissue	Pritchard
rs12914501	CCDC32	cis	multi-tissue	Pritchard
rs12914501	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12914501	C15orf57	cis	Artery Tibial	GTEx
rs12914501	C15orf57	cis	Artery Aorta	GTEx
rs12914501	RP11-111A22.1	cis	Stomach	GTEx
rs12914501	C15orf57	cis	Lymphoblastoid	GTEx
rs12914501	RAD51	cis	multi-tissue	Pritchard
rs12914501	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12914501	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12914501	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs12914501	C15orf57	cis	lung	GTEx
rs12914501	C15orf57	cis	Cerebellum	GTEx
rs12914501	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12914501	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12914501	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12914501	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs12914501	C15orf57	cis	Esophagus Mucosa	GTEx
rs12914501	RP11-111A22.1	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr15:40863000-40870200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:40863200-40868600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:40863200-40868800	Weak transcription	Fetal Heart	heart
7	chr15:40863200-40869000	Weak transcription	Fetal Brain Male	brain
8	chr15:40864000-40868800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr15:40865800-40875000	Weak transcription	Fetal Lung	lung
10	chr15:40866000-40870000	Weak transcription	NH-A	brain
11	chr15:40866000-40874800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:40866400-40869000	Weak transcription	Fetal Kidney	kidney
13	chr15:40866400-40874800	Weak transcription	Colonic Mucosa	Colon
14	chr15:40866400-40876600	Weak transcription	HSMMtube	muscle
15	chr15:40866400-40878200	Weak transcription	Brain Angular Gyrus	brain
16	chr15:40866600-40868600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:40866600-40868600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:40866600-40868600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:40866600-40868800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:40866600-40869600	Weak transcription	Fetal Stomach	stomach
21	chr15:40866600-40870000	Weak transcription	Gastric	stomach
22	chr15:40866600-40870200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:40866600-40870600	Weak transcription	Esophagus	oesophagus
24	chr15:40866600-40871400	Weak transcription	Thymus	Thymus
25	chr15:40866600-40873600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:40866600-40873800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:40866600-40873800	Weak transcription	Fetal Intestine Small	intestine
28	chr15:40866600-40874600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:40866600-40874800	Weak transcription	Pancreas	Pancrea
30	chr15:40866600-40874800	Weak transcription	A549	lung
31	chr15:40866600-40875000	Weak transcription	Lung	lung
32	chr15:40866600-40875000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:40866600-40875200	Weak transcription	Spleen	Spleen
34	chr15:40866600-40875200	Weak transcription	HSMM	muscle
35	chr15:40866600-40881800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:40866600-40881800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:40866600-40881800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:40866800-40868600	Weak transcription	GM12878-XiMat	blood
39	chr15:40866800-40869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:40866800-40870000	Weak transcription	HUVEC	blood vessel
41	chr15:40866800-40871000	Weak transcription	HepG2	liver
42	chr15:40866800-40874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:40866800-40875200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:40866800-40875200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:40866800-40875200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:40867000-40868800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:40867000-40868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:40867000-40869000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:40867000-40869000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:40867000-40870000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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