Variant report

Variant	rs16973451
Chromosome Location	chr15:82464785-82464786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:82460625..82462392-chr15:82463596..82466044,2	MCF-7	breast:
2	chr15:82458770..82460757-chr15:82464173..82465930,2	K562	blood:
3	chr15:82463946..82466687-chr15:82468924..82471039,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1128431	0.90[ASN][1000 genomes]
rs11852244	0.90[ASN][1000 genomes]
rs11853682	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11855145	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856561	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16973420	0.88[ASN][1000 genomes]
rs16973453	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17354842	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292071	0.88[ASN][1000 genomes]
rs28529095	0.87[ASN][1000 genomes]
rs28539162	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28578791	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28675984	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28754625	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28883606	0.82[ASN][1000 genomes]
rs4725	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778983	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55914836	0.90[ASN][1000 genomes]
rs56394250	0.84[ASN][1000 genomes]
rs57014042	0.84[ASN][1000 genomes]
rs60855901	0.90[ASN][1000 genomes]
rs61203524	0.87[ASN][1000 genomes]
rs6495644	0.98[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66672254	0.88[ASN][1000 genomes]
rs66701409	0.90[ASN][1000 genomes]
rs67988426	0.80[ASN][1000 genomes]
rs71156029	0.88[ASN][1000 genomes]
rs7162177	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73451393	0.86[ASN][1000 genomes]
rs8023960	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032033	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034586	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040160	0.86[ASN][1000 genomes]
rs8042665	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920827	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs16973451	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs16973451	RP13-608F4.1	cis	Stomach	GTEx
rs16973451	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs16973451	AP3B2	cis	Nerve Tibial	GTEx
rs16973451	AP3B2	cis	lung	GTEx
rs16973451	RP11-152F13.3	cis	Esophagus Mucosa	GTEx
rs16973451	FLJ22795///LOC727751	N/A	lymphoblastoid	RTeQTL
rs16973451	RP11-152F13.7	cis	lung	GTEx
rs16973451	RP11-152F13.3	cis	lung	GTEx
rs16973451	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs16973451	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82419200-82470600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:82439800-82465600	Weak transcription	K562	blood
5	chr15:82441400-82469600	Weak transcription	Fetal Brain Male	brain
6	chr15:82444400-82465200	Weak transcription	Brain Germinal Matrix	brain
7	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
8	chr15:82451000-82469800	Weak transcription	Psoas Muscle	Psoas
9	chr15:82452600-82470600	Weak transcription	Esophagus	oesophagus
10	chr15:82455400-82466600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:82455400-82466800	Weak transcription	Brain Substantia Nigra	brain
12	chr15:82455400-82475200	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:82455400-82475200	Weak transcription	Pancreas	Pancrea
14	chr15:82455600-82469200	Weak transcription	Brain Anterior Caudate	brain
15	chr15:82455600-82475200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:82455800-82467200	Weak transcription	Spleen	Spleen
17	chr15:82455800-82469800	Weak transcription	Ovary	ovary
18	chr15:82456000-82469800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:82456000-82475800	Weak transcription	Lung	lung
21	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
22	chr15:82456200-82469000	Weak transcription	Osteobl	bone
23	chr15:82456200-82469600	Weak transcription	HSMMtube	muscle
24	chr15:82456200-82470000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:82456200-82475200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
27	chr15:82456400-82469400	Weak transcription	HSMM	muscle
28	chr15:82456400-82470600	Weak transcription	Left Ventricle	heart
29	chr15:82456400-82473000	Weak transcription	Fetal Intestine Large	intestine
30	chr15:82456400-82474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:82456400-82475200	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:82456400-82475200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:82456400-82502800	Weak transcription	Gastric	stomach
41	chr15:82456400-82505400	Weak transcription	Dnd41	blood
42	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:82456600-82466600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:82456600-82466600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:82456600-82466800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:82456600-82474200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:82456600-82474400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:82456600-82474400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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