Variant report

Variant	rs34862454
Chromosome Location	chr15:75101530-75101531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr15:75101345-75101580	HepG2	liver:	n/a	n/a
2	CTCF	chr15:75101323-75101619	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:75101300-75101569	HepG2	liver:	n/a	n/a
4	CTCF	chr15:75101209-75101566	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr15:75101333-75101537	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr15:75101420-75101570	SAEC	small airway:	n/a	n/a
7	CTCF	chr15:75101380-75101530	A549	lung:	n/a	n/a
8	CTCF	chr15:75101316-75101581	K562	blood:	n/a	n/a
9	RAD21	chr15:75101177-75101724	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr15:75101380-75101530	HPF	lung:	n/a	n/a
11	ZNF263	chr15:75101210-75101659	HEK293-T-REx	kidney:	n/a	n/a
12	CTCF	chr15:75101400-75101550	HCM	heart:	n/a	n/a
13	CTCF	chr15:75101420-75101570	HCT-116	colon:	n/a	n/a
14	CTCF	chr15:75101380-75101530	GM12865	blood:	n/a	n/a
15	RAD21	chr15:75101204-75101677	MCF-7	breast:	n/a	n/a
16	CTCF	chr15:75101380-75101530	GM12873	blood:	n/a	n/a
17	CTCF	chr15:75101400-75101550	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr15:75101380-75101530	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr15:75101346-75101546	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr15:75101420-75101570	HMF	breast:	n/a	n/a
21	CTCF	chr15:75101460-75101610	Caco-2	colon:	n/a	n/a
22	CTCF	chr15:75101380-75101530	MCF-7	breast:	n/a	n/a
23	CTCF	chr15:75101380-75101530	BE2_C	brain:	n/a	n/a
24	CTCF	chr15:75101420-75101570	GM12870	blood:	n/a	n/a
25	CTCF	chr15:75101400-75101550	GM12871	blood:	n/a	n/a
26	CTCF	chr15:75101341-75101536	K562	blood:	n/a	n/a
27	CTCF	chr15:75101400-75101550	HFF-Myc	foreskin:	n/a	n/a
28	CTCF	chr15:75101380-75101530	HBMEC	blood vessel:	n/a	n/a
29	RAD21	chr15:75101271-75101645	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr15:75101420-75101570	HAc	cerebellar:	n/a	n/a
31	CTCF	chr15:75101400-75101550	RPTEC	kidney:	n/a	n/a
32	CTCF	chr15:75101420-75101570	Caco-2	colon:	n/a	n/a
33	ZNF143	chr15:75101254-75101589	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr15:75101400-75101550	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr15:75101277-75101589	K562	blood:	n/a	n/a
36	RAD21	chr15:75101281-75101548	HepG2	liver:	n/a	n/a
37	CTCF	chr15:75101380-75101530	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr15:75101380-75101530	HMF	breast:	n/a	n/a
39	POLR2A	chr15:75101247-75101804	GM12891	blood:	n/a	n/a
40	CTCF	chr15:75101380-75101530	GM12864	blood:	n/a	n/a
41	CTCF	chr15:75101420-75101570	HRPEpiC	eye:	n/a	n/a
42	CTCF	chr15:75101380-75101530	NHEK	skin:	n/a	n/a
43	CTCF	chr15:75101268-75101610	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr15:75101224-75101627	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr15:75101214-75101645	K562	blood:	n/a	n/a
46	CTCF	chr15:75101400-75101550	HA-sp	spinal cord:	n/a	n/a
47	CTCF	chr15:75101304-75101584	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75101293..75104748-chr15:75109733..75112723,4	K562	blood:
2	chr15:75059199..75061491-chr15:75101386..75103400,2	MCF-7	breast:
3	chr15:75101475..75103116-chr15:75104529..75106195,2	K562	blood:
4	chr15:75080438..75082798-chr15:75099156..75102028,3	K562	blood:
5	chr15:75092440..75094935-chr15:75099537..75102010,2	MCF-7	breast:

No data

Variant related genes	Relation type
LMAN1L	TF binding region
ENSG00000264386	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11072507	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11072508	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632414	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11635664	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636952	0.81[EUR][1000 genomes]
rs12591513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903541	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12903896	0.82[AMR][1000 genomes]
rs12905199	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909307	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12917376	0.98[ASN][1000 genomes]
rs1378940	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378941	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1378942	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168518	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470890	0.84[AMR][1000 genomes]
rs2472304	0.84[AMR][1000 genomes]
rs2960192	0.84[AMR][1000 genomes]
rs35206230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784789	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886410	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62006567	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34862454	SCAMP5	cis	Artery Tibial	GTEx
rs34862454	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs34862454	SCAMP5	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
2	chr15:75095800-75101600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:75096000-75109000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:75096200-75105200	Weak transcription	Fetal Lung	lung
5	chr15:75096200-75109600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:75096400-75104800	Weak transcription	Right Ventricle	heart
7	chr15:75096600-75102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:75096600-75107200	Weak transcription	Gastric	stomach
9	chr15:75096600-75107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:75096800-75101600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:75096800-75101600	Weak transcription	NHDF-Ad	bronchial
12	chr15:75096800-75101800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75096800-75101800	Weak transcription	HSMM	muscle
14	chr15:75096800-75102000	Weak transcription	NHLF	lung
15	chr15:75096800-75102200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:75096800-75102400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:75096800-75104800	Weak transcription	Ovary	ovary
18	chr15:75096800-75107200	Weak transcription	Pancreas	Pancrea
19	chr15:75096800-75107200	Weak transcription	A549	lung
20	chr15:75096800-75107400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:75096800-75107400	Weak transcription	HSMMtube	muscle
22	chr15:75096800-75109000	Weak transcription	Fetal Intestine Large	intestine
23	chr15:75096800-75109200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:75096800-75109400	Weak transcription	HUVEC	blood vessel
25	chr15:75096800-75109800	Weak transcription	NH-A	brain
26	chr15:75097000-75101600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:75097000-75101600	Weak transcription	Primary B cells from cord blood	blood
28	chr15:75097000-75102800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:75097000-75107200	Weak transcription	Spleen	Spleen
30	chr15:75097000-75107600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:75097000-75109200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:75097000-75109400	Weak transcription	Brain Anterior Caudate	brain
33	chr15:75097200-75101800	Weak transcription	Osteobl	bone
34	chr15:75097200-75108000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:75097200-75109400	Weak transcription	Lung	lung
36	chr15:75097600-75101800	Weak transcription	Fetal Brain Female	brain
37	chr15:75097600-75103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:75097600-75108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:75097600-75111000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:75097800-75101800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:75097800-75107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:75097800-75109200	Weak transcription	Brain Germinal Matrix	brain
43	chr15:75098000-75101800	Weak transcription	Fetal Intestine Small	intestine
44	chr15:75098800-75102000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:75099000-75101800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:75099200-75101800	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr15:75099200-75102000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr15:75099200-75102200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr15:75099400-75101600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr15:75099400-75102200	Enhancers	Primary T helper cells fromperipheralblood	blood

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