Variant report

Variant	rs17464903
Chromosome Location	chr15:77195486-77195487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77195051..77197848-chr15:77221697..77224553,2	MCF-7	breast:
2	chr15:77195486..77197689-chr15:77712877..77715018,2	K562	blood:
3	chr15:77194744..77199863-chr15:77220881..77225601,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140382	Chromatin interaction
ENSG00000117906	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1116535	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12148386	0.85[ASN][1000 genomes]
rs12438362	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12441855	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595586	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909665	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912465	0.82[YRI][hapmap]
rs12913810	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916324	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471780	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17380507	1.00[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2137307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2404602	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs2469204	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs34338978	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748201	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35076986	1.00[ASN][1000 genomes]
rs35157989	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35999717	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829489	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4360890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4383105	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4442773	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4641709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4886503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4886507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886829	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4886839	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56234001	0.92[ASN][1000 genomes]
rs58889902	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66508953	0.86[ASN][1000 genomes]
rs71398948	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166156	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8024737	0.86[ASN][1000 genomes]
rs8028294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8040539	0.85[JPT][hapmap]
rs9788684	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv1803942	chr15:77151005-77210457	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17464903	SCAPER	cis	Thyroid	GTEx
rs17464903	SCAPER	cis	cerebellum	SCAN
rs17464903	NRG4	cis	parietal	SCAN
rs17464903	SCAPER	cis	Artery Tibial	GTEx
rs17464903	SCAPER	cis	parietal	SCAN
rs17464903	STOML1	cis	cerebellum	SCAN
rs17464903	SCAPER	cis	Nerve Tibial	GTEx
rs17464903	SCAPER	cis	lung	GTEx
rs17464903	ZNF291	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77112200-77196000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:77133200-77196800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:77140800-77195800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:77142000-77195800	Weak transcription	Right Ventricle	heart
5	chr15:77146400-77196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:77148600-77195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:77148800-77195600	Weak transcription	Dnd41	blood
8	chr15:77158800-77195600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:77158800-77195600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:77168600-77195600	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:77168600-77196800	Weak transcription	Pancreas	Pancrea
12	chr15:77168600-77196800	Weak transcription	Spleen	Spleen
13	chr15:77172800-77195600	Weak transcription	HSMM	muscle
14	chr15:77175600-77196800	Weak transcription	Aorta	Aorta
15	chr15:77175600-77196800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:77175800-77195600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:77176000-77195800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:77176000-77196800	Weak transcription	Ovary	ovary
19	chr15:77176200-77195800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:77176400-77195600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:77179400-77196000	Weak transcription	Thymus	Thymus
22	chr15:77179800-77195600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:77180000-77196800	Weak transcription	Lung	lung
24	chr15:77184400-77195800	Weak transcription	Primary T cells from cord blood	blood
25	chr15:77186800-77195800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:77189000-77195600	Weak transcription	Brain Substantia Nigra	brain
27	chr15:77189200-77196800	Weak transcription	Gastric	stomach
28	chr15:77190200-77196800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:77190200-77196800	Weak transcription	Esophagus	oesophagus
30	chr15:77191000-77196800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:77191200-77195600	Weak transcription	NHEK	skin
32	chr15:77191200-77195800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:77191200-77195800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:77191600-77196600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:77191800-77195600	Weak transcription	Placenta	Placenta
36	chr15:77191800-77195800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:77191800-77196000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:77192000-77196600	Weak transcription	Fetal Stomach	stomach
39	chr15:77193000-77195800	Weak transcription	Brain Anterior Caudate	brain
40	chr15:77193000-77196800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:77193200-77195600	Weak transcription	Fetal Heart	heart
42	chr15:77193200-77195600	Weak transcription	Fetal Intestine Large	intestine
43	chr15:77193200-77195600	Weak transcription	A549	lung
44	chr15:77193200-77195800	Weak transcription	Fetal Thymus	thymus
45	chr15:77193200-77195800	Weak transcription	Right Atrium	heart
46	chr15:77193200-77196000	Weak transcription	Fetal Brain Female	brain
47	chr15:77193400-77195600	Weak transcription	K562	blood
48	chr15:77194600-77195600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:77194600-77196000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr15:77194800-77195600	Weak transcription	Fetal Intestine Small	intestine

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