Variant report

Variant	rs12916323
Chromosome Location	chr15:40827030-40827031
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40825965..40829345-chr15:40829678..40833688,6	K562	blood:
2	chr15:40825263..40828833-chr15:40829678..40833530,4	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1051482	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10851396	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070275	0.80[CEU][hapmap]
rs11070279	0.91[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070280	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11852479	0.81[EUR][1000 genomes]
rs11852527	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11857247	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12148185	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12899408	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12907448	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12907984	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12908114	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908867	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12914501	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12915563	0.87[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1453183	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17746659	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17747399	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1901774	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123534	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412524	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2412545	0.87[CEU][hapmap]
rs3213999	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34303240	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34750756	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35030447	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35884042	0.82[AMR][1000 genomes]
rs36122190	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3743146	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3803353	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4457966	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs4924478	0.80[CEU][hapmap]
rs5030783	0.88[CEU][hapmap]
rs55954396	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56384845	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61048252	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62018030	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62018046	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62018048	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62018051	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62019866	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62019883	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7162749	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7164385	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7165054	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7181909	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72733469	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs731640	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733299	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8025458	0.96[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8028910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036938	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8042733	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9806410	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs999197	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][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	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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12916323	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12916323	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs12916323	CCDC32	cis	normal skin	skin_eQTL
rs12916323	C15orf57	cis	Cerebellum	GTEx
rs12916323	ZFYVE19	cis	multi-tissue	Pritchard
rs12916323	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12916323	C15orf57	cis	Esophagus Muscularis	GTEx
rs12916323	CCDC32	cis	lesional skin	skin_eQTL
rs12916323	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12916323	C15orf57	cis	Artery Tibial	GTEx
rs12916323	CCDC32	cis	multi-tissue	Pritchard
rs12916323	C15orf57	cis	Nerve Tibial	GTEx
rs12916323	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12916323	MGC20481	cis	multi-tissue	Pritchard
rs12916323	RP11-111A22.1	cis	lung	GTEx
rs12916323	C15orf57	cis	lung	GTEx
rs12916323	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40805200-40828200	Weak transcription	Placenta	Placenta
2	chr15:40805200-40833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:40812400-40828600	Weak transcription	Primary T cells from cord blood	blood
4	chr15:40812400-40828600	Weak transcription	Right Ventricle	heart
5	chr15:40812400-40828800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:40812400-40828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:40812400-40829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:40812400-40829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:40812400-40831000	Weak transcription	Thymus	Thymus
10	chr15:40812400-40837800	Weak transcription	Lung	lung
11	chr15:40812600-40831400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:40812600-40840600	Weak transcription	Hela-S3	cervix
13	chr15:40816800-40835000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:40816800-40845600	Weak transcription	Ovary	ovary
15	chr15:40818200-40828000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:40818400-40828200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:40819200-40831200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:40819400-40828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:40819400-40830200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40819400-40831200	Weak transcription	Gastric	stomach
21	chr15:40819600-40845000	Weak transcription	Pancreas	Pancrea
22	chr15:40820800-40833800	Weak transcription	K562	blood
23	chr15:40821200-40828800	Weak transcription	Fetal Intestine Small	intestine
24	chr15:40821400-40827800	Weak transcription	Fetal Stomach	stomach
25	chr15:40821400-40836800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr15:40821400-40848000	Weak transcription	Brain Anterior Caudate	brain
27	chr15:40821800-40840400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:40822600-40831400	Weak transcription	Aorta	Aorta
30	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
31	chr15:40822800-40831200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:40823200-40839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:40823800-40841800	Weak transcription	Brain Substantia Nigra	brain
34	chr15:40824800-40842600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:40825000-40836200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:40825200-40830400	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:40825400-40830400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr15:40825600-40839400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:40825600-40840000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:40825800-40829000	Weak transcription	NHLF	lung
41	chr15:40825800-40839200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:40825800-40839600	Weak transcription	NHEK	skin
43	chr15:40826200-40827200	ZNF genes & repeats	GM12878-XiMat	blood
44	chr15:40826200-40828000	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:40826200-40828200	Weak transcription	Fetal Lung	lung
46	chr15:40826200-40831400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:40826400-40827200	Enhancers	Primary B cells from peripheral blood	blood
48	chr15:40826600-40827400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:40826600-40831200	Weak transcription	Adipose Nuclei	Adipose
50	chr15:40827000-40827400	Strong transcription	Spleen	Spleen

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