Variant report

Variant	rs8039755
Chromosome Location	chr15:75337426-75337427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75334181-75340414	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75334930-75337701	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:75333297-75341736	GM12878	blood:	n/a	n/a
4	RUNX3	chr15:75337358-75338182	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:75335006-75337519	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:75337284-75337883	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:75335034-75337858	GM12878	blood:	n/a	n/a
8	RUNX3	chr15:75337420-75338238	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75336500-75337437	GM12891	blood:	n/a	n/a
10	STAT5A	chr15:75337278-75338281	GM12878	blood:	n/a	n/a
11	MTA3	chr15:75334888-75340698	GM12878	blood:	n/a	n/a
12	PML	chr15:75337321-75338265	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:75333262-75344076	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75337368-75338297	GM12892	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75318584..75321988-chr15:75334747..75339188,4	K562	blood:
3	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
4	chr15:75335868..75337626-chr15:75660366..75661953,2	MCF-7	breast:
5	chr15:75336184..75338674-chr15:75501578..75503500,2	K562	blood:
6	chr15:75337101..75339665-chr15:75342536..75344490,2	MCF-7	breast:
7	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:
8	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
9	chr15:75337372..75339109-chr15:75499292..75501043,2	K562	blood:
10	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

No data

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11854975	0.86[EUR][1000 genomes]
rs12101482	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593566	0.90[YRI][hapmap]
rs12899062	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12900654	0.90[YRI][hapmap]
rs12904227	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909515	0.85[AFR][1000 genomes]
rs12917120	0.93[YRI][hapmap]
rs13056	0.92[YRI][hapmap]
rs1867148	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867151	0.80[AFR][1000 genomes]
rs2083730	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2120019	0.93[YRI][hapmap]
rs2304899	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs2304902	0.83[EUR][1000 genomes]
rs2304903	0.83[YRI][hapmap]
rs34582157	0.81[ASN][1000 genomes]
rs35078352	0.84[EUR][1000 genomes]
rs3812944	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs4886417	0.82[EUR][1000 genomes]
rs4886651	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4886652	0.83[AFR][1000 genomes]
rs4886655	0.84[EUR][1000 genomes]
rs6495143	0.90[YRI][hapmap]
rs6495144	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495150	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495151	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67168917	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163362	0.81[EUR][1000 genomes]
rs7163636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167261	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181261	0.82[EUR][1000 genomes]
rs8028632	0.93[YRI][hapmap]
rs8030089	0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8039755	SCAMP5	cis	Artery Tibial	GTEx
rs8039755	SCAMP5	cis	lung	GTEx
rs8039755	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75316800-75338800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
3	chr15:75322200-75339000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:75322400-75339200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:75322600-75338600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:75324600-75339200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:75328600-75338800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:75329200-75338800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:75330600-75340000	Weak transcription	NHEK	skin
13	chr15:75333600-75338400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:75334000-75344600	Enhancers	Placenta	Placenta
16	chr15:75334200-75340400	Genic enhancers	Fetal Intestine Small	intestine
17	chr15:75334200-75340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
19	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
20	chr15:75334600-75340400	Enhancers	Liver	Liver
21	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
22	chr15:75334600-75341000	Enhancers	Lung	lung
23	chr15:75334600-75343200	Enhancers	Right Atrium	heart
24	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
25	chr15:75335000-75337600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:75335000-75340200	Enhancers	Primary T cells fromperipheralblood	blood
27	chr15:75335000-75340400	Enhancers	Fetal Thymus	thymus
28	chr15:75335200-75337600	Enhancers	Ovary	ovary
29	chr15:75335200-75338200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:75335200-75340200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
32	chr15:75335600-75339000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:75335600-75339200	Weak transcription	Fetal Kidney	kidney
34	chr15:75335600-75340400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr15:75335800-75337600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:75335800-75338800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:75335800-75338800	Weak transcription	Aorta	Aorta
38	chr15:75335800-75339000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:75335800-75339000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:75335800-75339400	Flanking Active TSS	GM12878-XiMat	blood
41	chr15:75335800-75340600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr15:75336000-75338200	Strong transcription	Thymus	Thymus
43	chr15:75336000-75339000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:75336000-75340200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:75336200-75338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:75336200-75339000	Weak transcription	A549	lung
48	chr15:75336400-75337800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:75336400-75337800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:75336400-75337800	Genic enhancers	HepG2	liver

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