Variant report

Variant	rs1480503
Chromosome Location	chr15:30073215-30073216
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	chr15:30072029..30073605-chr15:30114260..30117133,2	K562	blood:

Variant related genes	Relation type
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10775231	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11073205	0.93[EUR][1000 genomes]
rs11073218	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs11636849	0.83[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs12438925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12440211	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12440708	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441554	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1383315	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552077	0.82[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1585900	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1679647	0.86[ASN][1000 genomes]
rs17750802	0.88[CHB][hapmap]
rs1871678	0.83[ASN][1000 genomes]
rs2032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2229518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2306437	0.88[CHB][hapmap]
rs2337167	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs260531	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260532	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260533	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260534	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs260538	0.81[ASN][1000 genomes]
rs28675809	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2878893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2878905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809503	0.88[CHB][hapmap]
rs4073316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4362339	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4779670	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4780258	0.84[ASN][1000 genomes]
rs4780259	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4780260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4780263	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495890	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6495914	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495927	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495935	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495945	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7166786	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7168919	0.87[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170406	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7171815	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175819	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176594	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7180387	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767514	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs785445	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs785446	0.83[CEU][hapmap]
rs8023974	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8027827	0.81[EUR][1000 genomes];0.89[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	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1480503	C15orf2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
2	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:30058600-30092200	Weak transcription	Esophagus	oesophagus
4	chr15:30058600-30106000	Weak transcription	Gastric	stomach
5	chr15:30059800-30086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:30060800-30076800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:30062800-30096600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:30063600-30073400	Weak transcription	Fetal Lung	lung
9	chr15:30063800-30076800	Weak transcription	Fetal Kidney	kidney
10	chr15:30063800-30096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:30063800-30096800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:30064000-30085600	Weak transcription	Fetal Stomach	stomach
13	chr15:30064000-30085800	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:30064200-30073600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:30064400-30083800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
17	chr15:30065600-30085400	Weak transcription	Fetal Intestine Large	intestine
18	chr15:30065600-30090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:30065600-30094400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:30065600-30094400	Weak transcription	Fetal Intestine Small	intestine
21	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
22	chr15:30067400-30075400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:30067400-30097400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:30067600-30080600	Weak transcription	NHLF	lung
25	chr15:30067800-30075800	Weak transcription	HUVEC	blood vessel
26	chr15:30067800-30076600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:30067800-30076800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:30068600-30076800	Weak transcription	Osteobl	bone
29	chr15:30069000-30075400	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:30069400-30075600	Weak transcription	NHEK	skin
31	chr15:30069600-30075200	Weak transcription	Ovary	ovary
32	chr15:30069600-30076600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:30071200-30080600	Weak transcription	Liver	Liver
34	chr15:30071200-30090000	Weak transcription	Adipose Nuclei	Adipose
35	chr15:30071600-30073400	Weak transcription	Brain Substantia Nigra	brain
36	chr15:30071600-30073400	Weak transcription	Right Ventricle	heart
37	chr15:30071600-30074400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:30071600-30075600	Weak transcription	Left Ventricle	heart
39	chr15:30071600-30077200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:30071800-30077200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:30071800-30077400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:30071800-30077400	Weak transcription	Psoas Muscle	Psoas
43	chr15:30071800-30081400	Weak transcription	Fetal Heart	heart
44	chr15:30071800-30097600	Weak transcription	K562	blood
45	chr15:30072200-30073600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr15:30072200-30075800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:30072200-30077400	Weak transcription	Brain Anterior Caudate	brain
48	chr15:30072400-30073600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:30072400-30074200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:30072400-30076800	Weak transcription	HSMM	muscle

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