Variant report

Variant	rs17354842
Chromosome Location	chr15:82469600-82469601
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:82469573-82469899	NB4	blood:	n/a	chr15:82469708-82469718 chr15:82469709-82469719
2	MYC	chr15:82469575-82469888	MCF10A-Er-Src	breast:	n/a	chr15:82469708-82469718 chr15:82469709-82469719
3	MYC	chr15:82469572-82469909	NB4	blood:	n/a	chr15:82469708-82469718 chr15:82469709-82469719
4	MYC	chr15:82469596-82469891	MCF10A-Er-Src	breast:	n/a	chr15:82469708-82469718 chr15:82469709-82469719

No.	Distal block	Cell Line	Cell type
1	chr15:82456960..82458670-chr15:82467666..82470258,2	MCF-7	breast:
2	chr15:82463946..82466687-chr15:82468924..82471039,2	K562	blood:
3	chr15:82468744..82470564-chr15:82476578..82478505,2	K562	blood:

Variant related genes	Relation type
RNU1-77P	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1128431	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11852244	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11853682	0.89[ASN][1000 genomes]
rs11854157	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs11855145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11856561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973420	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16973451	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16973453	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292071	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs28529095	0.84[ASN][1000 genomes]
rs28539162	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28578791	0.82[ASN][1000 genomes]
rs28665836	0.80[ASN][1000 genomes]
rs28675984	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28754625	0.84[ASN][1000 genomes]
rs28883606	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3973890	0.90[JPT][hapmap]
rs4725	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4778983	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55914836	0.86[ASN][1000 genomes]
rs56394250	0.81[ASN][1000 genomes]
rs57014042	0.81[ASN][1000 genomes]
rs60855901	0.86[ASN][1000 genomes]
rs61203524	0.83[ASN][1000 genomes]
rs6495644	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66672254	0.84[ASN][1000 genomes]
rs66701409	0.86[ASN][1000 genomes]
rs71156029	0.84[ASN][1000 genomes]
rs7162177	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73451393	0.83[ASN][1000 genomes]
rs8023960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028284	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs8032033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034586	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8040160	0.82[ASN][1000 genomes]
rs8042665	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920827	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs17354842	RP11-152F13.3	cis	lung	GTEx
rs17354842	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs17354842	RP11-152F13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17354842	RP11-152F13.7	cis	Esophagus Mucosa	GTEx
rs17354842	RP11-152F13.7	cis	lung	GTEx
rs17354842	RP11-152F13.7	cis	Skin Sun Exposed Lower leg	GTEx
rs17354842	RP11-152F13.3	cis	Esophagus Mucosa	GTEx
rs17354842	AP3B2	cis	Nerve Tibial	GTEx
rs17354842	RP13-608F4.1	cis	Stomach	GTEx

Chromatin state (count:85 , 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	chr15:82441400-82469600	Weak transcription	Fetal Brain Male	brain
5	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
6	chr15:82451000-82469800	Weak transcription	Psoas Muscle	Psoas
7	chr15:82452600-82470600	Weak transcription	Esophagus	oesophagus
8	chr15:82455400-82475200	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:82455400-82475200	Weak transcription	Pancreas	Pancrea
10	chr15:82455600-82475200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:82455800-82469800	Weak transcription	Ovary	ovary
12	chr15:82456000-82469800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:82456000-82475800	Weak transcription	Lung	lung
15	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
16	chr15:82456200-82469600	Weak transcription	HSMMtube	muscle
17	chr15:82456200-82470000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:82456200-82475200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
20	chr15:82456400-82470600	Weak transcription	Left Ventricle	heart
21	chr15:82456400-82473000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:82456400-82474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:82456400-82475200	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:82456400-82475200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:82456400-82502800	Weak transcription	Gastric	stomach
33	chr15:82456400-82505400	Weak transcription	Dnd41	blood
34	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:82456600-82474200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr15:82456600-82474400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:82456600-82474400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:82456800-82475200	Weak transcription	Liver	Liver
42	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:82457000-82469800	Weak transcription	Aorta	Aorta
44	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:82458600-82475600	Weak transcription	GM12878-XiMat	blood
46	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:82458800-82469600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:82460800-82474000	Weak transcription	Adipose Nuclei	Adipose
50	chr15:82460800-82475200	Weak transcription	Primary T cells from cord blood	blood

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