Variant report

Variant	rs2914674
Chromosome Location	chr5:89769194-89769195
allele	A/C
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	MAFK	chr5:89768418-89769702	GM12878	blood:	n/a	chr5:89768782-89768797
2	KAP1	chr5:89768970-89771055	HEK293	kidney:	n/a	n/a
3	TBP	chr5:89768894-89771288	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:89769018-89769641	K562	blood:	n/a	n/a
5	TBP	chr5:89769047-89770954	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAFF	chr5:89768570-89769270	K562	blood:	n/a	chr5:89768780-89768798
7	USF2	chr5:89768963-89769561	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:89769089-89770975	NB4	blood:	n/a	n/a
9	MAZ	chr5:89769006-89771106	IMR90	lung:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
10	BACH1	chr5:89769103-89771002	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr5:89769068-89771039	Hela-S3	cervix:	n/a	n/a
12	E2F6	chr5:89769070-89771102	K562	blood:	n/a	n/a
13	POLR2A	chr5:89769058-89770947	K562	blood:	n/a	n/a
14	HEY1	chr5:89768926-89769657	K562	blood:	n/a	n/a
15	CHD2	chr5:89769110-89770896	K562	blood:	n/a	n/a
16	POLR2A	chr5:89769032-89771013	K562	blood:	n/a	n/a
17	MAX	chr5:89769021-89771203	HepG2	liver:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
18	POLR2A	chr5:89769113-89770990	GM18505	blood:	n/a	n/a
19	MAFK	chr5:89768596-89769238	HepG2	liver:	n/a	chr5:89768782-89768797
20	POLR2A	chr5:89769061-89769610	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr5:89769017-89771079	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:89768999-89771072	GM12892	blood:	n/a	n/a
23	MYC	chr5:89769071-89771203	K562	blood:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
24	BRCA1	chr5:89768969-89769720	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr5:89768908-89771346	MCF10A-Er-Src	breast:	n/a	n/a
26	TCF7L2	chr5:89768971-89770924	Hela-S3	cervix:	n/a	n/a
27	SMARCB1	chr5:89769094-89771066	Hela-S3	cervix:	n/a	n/a
28	CUX1	chr5:89768552-89769386	K562	blood:	n/a	n/a
29	POLR2A	chr5:89768952-89770824	K562	blood:	n/a	n/a
30	MAZ	chr5:89769120-89769408	GM12878	blood:	n/a	n/a
31	MAX	chr5:89769065-89771142	NB4	blood:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
32	MAX	chr5:89769143-89771145	MCF-7	breast:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
33	POLR2A	chr5:89769156-89769630	PFSK-1	brain:	n/a	n/a
34	STAT3	chr5:89768930-89769489	MCF10A-Er-Src	breast:	n/a	n/a
35	RFX5	chr5:89768853-89769400	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr5:89769077-89769323	Hela-S3	cervix:	n/a	n/a
37	SMARCC1	chr5:89769153-89771072	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr5:89768984-89771007	H1-hESC	embryonic stem cell:	n/a	n/a
39	CEBPB	chr5:89769008-89769474	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr5:89769190-89771256	Hela-S3	cervix:	n/a	chr5:89770897-89770906
41	YY1	chr5:89769104-89769507	H1-hESC	embryonic stem cell:	n/a	n/a
42	MYC	chr5:89768858-89771510	MCF10A-Er-Src	breast:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
43	MTA3	chr5:89768971-89769571	GM12878	blood:	n/a	n/a
44	MAZ	chr5:89768906-89771043	K562	blood:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
45	RFX5	chr5:89769105-89769382	HepG2	liver:	n/a	n/a
46	MYC	chr5:89769053-89771063	K562	blood:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
47	POLR2A	chr5:89768886-89771418	MCF10A-Er-Src	breast:	n/a	n/a
48	MYC	chr5:89769159-89771095	K562	blood:	n/a	chr5:89770655-89770665 chr5:89770897-89770908 chr5:89770234-89770244 chr5:89770899-89770906 chr5:89770897-89770907
49	MXI1	chr5:89769088-89771258	IMR90	lung:	n/a	chr5:89770897-89770906
50	HCFC1	chr5:89768678-89771042	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89769110..89772331-chr5:90086907..90091587,4	K562	blood:
2	chr5:89704491..89706992-chr5:89769088..89771566,3	MCF-7	breast:
3	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
4	chr5:89702524..89708084-chr5:89764247..89773389,22	K562	blood:
5	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:
6	chr5:89768685..89771799-chr5:89852676..89855842,6	MCF-7	breast:
7	chr5:89768584..89771978-chr5:90675764..90678297,3	K562	blood:
8	chr5:89768691..89773005-chr5:89822332..89827140,9	MCF-7	breast:
9	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
10	chr5:89764343..89768380-chr5:89768675..89771583,10	MCF-7	breast:
11	chr5:89701553..89708894-chr5:89768084..89771807,14	K562	blood:
12	chr5:89769121..89772256-chr5:89935164..89938437,4	K562	blood:
13	chr5:89703543..89706963-chr5:89767513..89771420,6	MCF-7	breast:

Variant related genes	Relation type
POLR3G	TF binding region
ENSG00000113356	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10214167	0.84[JPT][hapmap]
rs10942594	0.84[JPT][hapmap]
rs12519370	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303801	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2914676	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763070	0.84[JPT][hapmap]
rs3763072	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4343874	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6867534	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs6872360	0.84[JPT][hapmap]
rs7721640	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7729481	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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 miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv518131	chr5:89748142-89781594	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2914674	C5orf36	cis	parietal	SCAN
rs2914674	GPR98	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89752000-89769200	Weak transcription	Small Intestine	intestine
2	chr5:89758000-89769200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:89767800-89769200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:89768200-89771400	Active TSS	GM12878-XiMat	blood
5	chr5:89768400-89769400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:89768400-89769400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr5:89768400-89769400	Flanking Active TSS	NHEK	skin
8	chr5:89768400-89770200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:89768400-89770400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr5:89768400-89771200	Active TSS	Brain Angular Gyrus	brain
11	chr5:89768600-89769200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
12	chr5:89768600-89769200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:89768600-89769200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:89768600-89769200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:89768600-89769200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:89768600-89769200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:89768600-89769400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr5:89768600-89769400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr5:89768600-89769400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr5:89768600-89769400	Flanking Active TSS	Hela-S3	cervix
21	chr5:89768600-89769600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:89768600-89769600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr5:89768600-89769600	Flanking Active TSS	Fetal Lung	lung
24	chr5:89768600-89769600	Flanking Active TSS	Dnd41	blood
25	chr5:89768600-89770000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:89768600-89770000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:89768600-89770800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:89768600-89771200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr5:89768600-89771600	Active TSS	NHDF-Ad	bronchial
30	chr5:89768600-89772000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr5:89768800-89769200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr5:89768800-89769200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:89768800-89769200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:89768800-89769200	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr5:89768800-89769200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr5:89768800-89769400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:89768800-89769400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:89768800-89769400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr5:89768800-89769400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr5:89768800-89769400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr5:89768800-89769400	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr5:89768800-89769400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr5:89768800-89769400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr5:89768800-89769400	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr5:89768800-89769400	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr5:89768800-89769400	Flanking Active TSS	HMEC	breast
47	chr5:89768800-89769400	Active TSS	HSMMtube	muscle
48	chr5:89768800-89769600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr5:89768800-89769600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr5:89768800-89769600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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