Variant report

Variant	rs12591175
Chromosome Location	chr15:75356073-75356074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75354485..75356101-chr15:75356641..75358451,2	K562	blood:
2	chr15:75335307..75337895-chr15:75354566..75358468,3	K562	blood:
3	chr15:75333748..75335630-chr15:75354954..75357925,2	MCF-7	breast:
4	chr15:75335307..75337637-chr15:75355852..75358468,2	K562	blood:

Variant related genes	Relation type
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12148355	0.80[ASN][1000 genomes]
rs12591994	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12592477	0.86[JPT][hapmap]
rs12593542	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs12594117	0.82[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289582	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2304904	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs28394281	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3743212	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs3812943	0.82[CEU][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3816261	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850093	0.83[LWK][hapmap]
rs3910748	0.85[ASW][hapmap];0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56970592	0.81[EUR][1000 genomes]
rs58294763	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58645417	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59303424	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61166993	0.84[EUR][1000 genomes]
rs6495135	0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.81[EUR][1000 genomes]
rs6495136	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6495137	0.81[EUR][1000 genomes]
rs6495138	0.82[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs6495140	0.84[EUR][1000 genomes]
rs6495142	0.82[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495146	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495148	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163390	0.82[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs7166105	0.85[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167415	0.82[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs7172715	0.82[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs7172989	0.81[EUR][1000 genomes]
rs7173218	0.85[ASW][hapmap];0.82[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7174129	0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.84[EUR][1000 genomes]
rs7175720	0.89[LWK][hapmap]
rs7177109	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181942	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs72475969	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7342591	0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.82[EUR][1000 genomes]
rs7342601	0.82[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs73432941	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73436579	0.81[EUR][1000 genomes]
rs73438537	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73438554	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73438569	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023908	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs74023935	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023936	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8024931	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8031545	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs8033125	0.96[ASN][1000 genomes]
rs8034149	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8038365	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039433	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9672996	0.84[EUR][1000 genomes]
rs9673012	0.82[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9788648	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12591175	SCAMP5	cis	lymphoblastoid	seeQTL
rs12591175	SCAMP5	cis	Thyroid	GTEx
rs12591175	SCAMP5	cis	Artery Tibial	GTEx
rs12591175	PPCDC	cis	Adipose Subcutaneous	GTEx
rs12591175	SCAMP5	cis	Esophagus Mucosa	GTEx
rs12591175	SCAMP5	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75340000-75360600	Weak transcription	Gastric	stomach
2	chr15:75340200-75359400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr15:75340800-75357600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:75341000-75356400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75341200-75357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:75342000-75357200	Weak transcription	Small Intestine	intestine
7	chr15:75342200-75357600	Weak transcription	Aorta	Aorta
8	chr15:75342400-75357400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:75342600-75357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:75342600-75357600	Weak transcription	Hela-S3	cervix
11	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:75342800-75357400	Weak transcription	Thymus	Thymus
13	chr15:75342800-75361600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:75343200-75357400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:75346400-75361600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:75347000-75356200	Weak transcription	Ovary	ovary
17	chr15:75347000-75364000	Weak transcription	Brain Substantia Nigra	brain
18	chr15:75350600-75357000	Weak transcription	Adipose Nuclei	Adipose
19	chr15:75351000-75357400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:75351000-75358200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:75351200-75356400	Weak transcription	Fetal Thymus	thymus
22	chr15:75351200-75356800	Weak transcription	Fetal Intestine Large	intestine
23	chr15:75351200-75357400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:75351200-75357600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:75351200-75357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:75351200-75358000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr15:75351200-75358000	Weak transcription	Right Ventricle	heart
28	chr15:75351200-75358000	Weak transcription	NHEK	skin
29	chr15:75351200-75358200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:75352400-75356600	Weak transcription	Fetal Intestine Small	intestine
31	chr15:75352400-75357000	Weak transcription	Fetal Stomach	stomach
32	chr15:75352400-75358000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:75353000-75357000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:75353600-75358400	Enhancers	Right Atrium	heart
35	chr15:75353800-75356400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:75353800-75357400	Weak transcription	K562	blood
37	chr15:75354000-75356400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:75354000-75356400	Weak transcription	Spleen	Spleen
39	chr15:75354000-75357000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:75354000-75357400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:75354000-75357600	Weak transcription	NH-A	brain
42	chr15:75354000-75357800	Weak transcription	Colonic Mucosa	Colon
43	chr15:75354200-75356600	Weak transcription	HSMMtube	muscle
44	chr15:75354200-75356800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:75354200-75357200	Weak transcription	HMEC	breast
46	chr15:75354200-75357200	Weak transcription	HSMM	muscle
47	chr15:75354200-75359000	Weak transcription	NHDF-Ad	bronchial
48	chr15:75354400-75357200	Enhancers	Left Ventricle	heart
49	chr15:75354400-75357600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:75354600-75357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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