Variant report

Variant	rs4362339
Chromosome Location	chr15:30005529-30005530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:29999465..30001395-chr15:30004096..30006646,2	K562	blood:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10152681	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10775231	0.94[CEU][hapmap]
rs11073205	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11073218	0.90[JPT][hapmap]
rs12438925	0.83[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440211	0.81[EUR][1000 genomes]
rs1383315	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1480503	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]
rs1552077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1585900	0.94[CEU][hapmap];0.84[MEX][hapmap]
rs1679647	0.91[ASN][1000 genomes]
rs1871678	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2229518	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2337167	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs260528	0.80[ASN][1000 genomes]
rs260529	0.80[ASN][1000 genomes]
rs260531	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs260532	0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs260533	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs260534	0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs260535	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs260538	0.97[ASN][1000 genomes]
rs2878893	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2878905	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3784353	0.87[LWK][hapmap]
rs4073316	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4780258	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4780259	0.94[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4780260	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6495890	0.84[EUR][1000 genomes]
rs6495914	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495927	0.80[ASN][1000 genomes]
rs6495935	0.80[ASN][1000 genomes]
rs6495945	0.94[CEU][hapmap]
rs7168919	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs7170406	0.94[CEU][hapmap]
rs7171815	0.80[ASN][1000 genomes]
rs7176476	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs7176594	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7180387	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs767514	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785445	0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8023974	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8027827	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4362339	C15orf2	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29989000-30014800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr15:29989600-30013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:29989600-30021200	Strong transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:29989600-30027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:29990000-30014200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:29990000-30016600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:29990200-30013600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:29990200-30016200	Strong transcription	Left Ventricle	heart
9	chr15:29990200-30028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:29990400-30014200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:29990400-30014400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:29990400-30014400	Strong transcription	Placenta	Placenta
13	chr15:29990400-30026400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr15:29990600-30014200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:29990800-30014400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:29991000-30014200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:29991200-30013800	Strong transcription	NH-A	brain
18	chr15:29991200-30014200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:29991200-30014400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:29991200-30014400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:29991200-30014600	Strong transcription	Osteobl	bone
22	chr15:29991200-30020200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:29991200-30022400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:29991400-30005800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr15:29991600-30014400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:29992000-30026600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:29992200-30014800	Weak transcription	Small Intestine	intestine
28	chr15:29993200-30019600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:29995600-30014200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:29996000-30014400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:29996200-30021400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:29997000-30006000	Weak transcription	Hela-S3	cervix
33	chr15:29998000-30013800	Strong transcription	Brain Anterior Caudate	brain
34	chr15:29999200-30014200	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:29999800-30007200	Weak transcription	Spleen	Spleen
36	chr15:30000000-30007200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:30000200-30010400	Weak transcription	Fetal Brain Female	brain
38	chr15:30000200-30010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:30000800-30007400	Weak transcription	Fetal Brain Male	brain
40	chr15:30001000-30006800	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:30001200-30008600	Weak transcription	Brain Germinal Matrix	brain
42	chr15:30001200-30013400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:30001400-30006200	Weak transcription	Lung	lung
44	chr15:30001400-30007200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:30001400-30007800	Weak transcription	Pancreas	Pancrea
46	chr15:30001400-30010200	Weak transcription	Colonic Mucosa	Colon
47	chr15:30001600-30007200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:30001600-30007200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:30001800-30006200	Weak transcription	Fetal Lung	lung
50	chr15:30001800-30007200	Weak transcription	Right Ventricle	heart

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