Variant report

Variant	rs1585900
Chromosome Location	chr15:30088636-30088637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:30087602..30089110-chr15:30112846..30115488,2	K562	blood:
2	chr15:30087643..30090373-chr15:30092334..30094638,2	K562	blood:
3	chr15:30086191..30088708-chr15:30102161..30104753,2	K562	blood:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction
ENSG00000259523	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10152681	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10519665	1.00[CHB][hapmap]
rs10775231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11073205	0.89[EUR][1000 genomes]
rs11636849	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[ASN][1000 genomes]
rs12438925	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs12440211	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12440708	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12441554	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1383315	0.93[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1480503	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]
rs1552077	0.94[CEU][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17671556	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs17671580	1.00[CHB][hapmap]
rs2032	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2035326	1.00[CHB][hapmap]
rs2229518	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs2291166	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2337167	0.89[CEU][hapmap]
rs2337170	0.84[ASN][1000 genomes]
rs260541	0.84[ASN][1000 genomes]
rs28675809	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2878893	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes]
rs2878905	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3784356	1.00[CHB][hapmap]
rs4073316	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4362339	0.94[CEU][hapmap];0.84[MEX][hapmap]
rs4779670	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4780259	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4780260	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4780263	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6495890	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6495914	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495927	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495935	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6495945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166786	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7168919	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171815	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7175819	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176476	0.93[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7176594	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs7180387	0.87[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs767514	0.93[ASW][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs785445	0.83[CEU][hapmap]
rs785446	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023974	0.81[EUR][1000 genomes]
rs8027827	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	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
10	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
rs1585900	C15orf2	cis	parietal	SCAN

Chromatin state (count:85 , 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	chr15:30062800-30096600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:30063800-30096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:30063800-30096800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
9	chr15:30065600-30090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:30065600-30094400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:30065600-30094400	Weak transcription	Fetal Intestine Small	intestine
12	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
13	chr15:30067400-30097400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:30071200-30090000	Weak transcription	Adipose Nuclei	Adipose
15	chr15:30071800-30097600	Weak transcription	K562	blood
16	chr15:30072800-30089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:30072800-30090000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:30072800-30091200	Weak transcription	Lung	lung
19	chr15:30072800-30092800	Weak transcription	Right Atrium	heart
20	chr15:30077600-30092400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:30078200-30090600	Weak transcription	Stomach Mucosa	stomach
22	chr15:30078200-30092800	Weak transcription	Psoas Muscle	Psoas
23	chr15:30078400-30090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:30078800-30092200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:30081600-30090600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:30081600-30097000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:30082200-30089400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:30082200-30094400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:30082400-30092000	Weak transcription	Brain Angular Gyrus	brain
30	chr15:30082400-30092000	Weak transcription	Brain Anterior Caudate	brain
31	chr15:30082400-30093200	Weak transcription	Right Ventricle	heart
32	chr15:30082400-30113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:30082600-30097000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:30083200-30092200	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:30084400-30089200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:30084600-30094200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:30085200-30090200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:30085800-30090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:30085800-30092800	Weak transcription	Fetal Stomach	stomach
40	chr15:30086000-30090000	Weak transcription	NHDF-Ad	bronchial
41	chr15:30086000-30092800	Weak transcription	NHLF	lung
42	chr15:30086000-30093000	Strong transcription	HSMM	muscle
43	chr15:30086000-30094000	Weak transcription	Left Ventricle	heart
44	chr15:30086000-30097000	Weak transcription	HSMMtube	muscle
45	chr15:30086000-30107600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:30086200-30089400	Weak transcription	Fetal Intestine Large	intestine
47	chr15:30086200-30090000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:30086200-30090400	Weak transcription	Osteobl	bone
49	chr15:30086200-30092200	Weak transcription	Fetal Lung	lung
50	chr15:30086200-30092600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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