Variant report

Variant	rs953555
Chromosome Location	chr15:75508276-75508277
allele	C/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	BCLAF1	chr15:75505652-75508826	GM12878	blood:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
2	POLR2A	chr15:75505563-75508929	ECC-1	luminal epithelium:	n/a	n/a
3	BCLAF1	chr15:75504465-75508533	GM12878	blood:	n/a	chr15:75504683-75504692 chr15:75507383-75507390 chr15:75507561-75507574
4	ZBTB7A	chr15:75507774-75508582	ECC-1	luminal epithelium:	n/a	chr15:75508470-75508478
5	POLR2A	chr15:75503968-75508962	GM18526	blood:	n/a	n/a
6	POLR2A	chr15:75503585-75508807	GM12891	blood:	n/a	n/a
7	EP300	chr15:75507893-75508418	ECC-1	luminal epithelium:	n/a	n/a
8	PAX5	chr15:75508089-75508931	GM12878	blood:	n/a	n/a
9	ELF1	chr15:75505530-75509026	GM12878	blood:	n/a	chr15:75505566-75505578
10	POLR2A	chr15:75505475-75509060	U87	brain:	n/a	n/a
11	POLR2A	chr15:75506292-75509098	U87	brain:	n/a	n/a
12	POLR2A	chr15:75503711-75508969	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:75503412-75508310	A549	lung:	n/a	n/a
14	TCF12	chr15:75507773-75508567	ECC-1	luminal epithelium:	n/a	chr15:75508311-75508321 chr15:75508312-75508319
15	BCL3	chr15:75506576-75508365	GM12878	blood:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
16	TCF12	chr15:75507657-75508582	ECC-1	luminal epithelium:	n/a	chr15:75508311-75508321 chr15:75508312-75508319
17	POLR2A	chr15:75504559-75509010	PFSK-1	brain:	n/a	n/a
18	CEBPB	chr15:75507940-75508391	ECC-1	luminal epithelium:	n/a	n/a
19	USF1	chr15:75507934-75508352	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr15:75499212-75509025	GM12892	blood:	n/a	n/a
21	POLR2A	chr15:75503799-75508816	GM12892	blood:	n/a	n/a
22	POLR2A	chr15:75501382-75508952	Hela-S3	cervix:	n/a	n/a
23	ATF2	chr15:75505713-75508426	GM12878	blood:	n/a	n/a
24	BCL3	chr15:75507052-75508658	A549	lung:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
25	FOSL2	chr15:75504754-75508851	HepG2	liver:	n/a	chr15:75506822-75506831
26	POLR2A	chr15:75499180-75510106	GM12892	blood:	n/a	n/a
27	POLR2A	chr15:75503447-75508620	K562	blood:	n/a	n/a
28	POLR2A	chr15:75505335-75508435	HCT-116	colon:	n/a	n/a
29	NFATC1	chr15:75504997-75509017	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:75508273-75508476	HepG2	liver:	n/a	n/a
31	RUNX3	chr15:75506487-75508451	GM12878	blood:	n/a	n/a
32	POLR2A	chr15:75507608-75508921	U87	brain:	n/a	n/a
33	NFIC	chr15:75507792-75508558	ECC-1	luminal epithelium:	n/a	n/a
34	BCL3	chr15:75505663-75508535	A549	lung:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
35	POU2F2	chr15:75504331-75508597	GM12891	blood:	n/a	chr15:75506170-75506182 chr15:75506167-75506179
36	POLR2A	chr15:75503496-75508425	HepG2	liver:	n/a	n/a
37	POU2F2	chr15:75507689-75508478	GM12878	blood:	n/a	n/a
38	NFIC	chr15:75507810-75508564	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr15:75503181-75509014	GM12892	blood:	n/a	n/a
40	POLR2A	chr15:75507334-75509020	ECC-1	luminal epithelium:	n/a	n/a
41	STAT5A	chr15:75508263-75509030	GM12878	blood:	n/a	chr15:75508442-75508454
42	RXRA	chr15:75507330-75508534	GM12878	blood:	n/a	chr15:75508108-75508122
43	POLR2A	chr15:75504935-75508761	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr15:75504321-75508791	GM12891	blood:	n/a	n/a
45	POLR2A	chr15:75507123-75508495	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr15:75503737-75510069	GM12878	blood:	n/a	n/a
47	MTA3	chr15:75507111-75508492	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:75504821-75509048	SK-N-MC	brain:	n/a	n/a
49	POLR2A	chr15:75503618-75508948	HL-60	blood:	n/a	n/a
50	ATF2	chr15:75506863-75508495	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75506671..75508576-chr15:75520216..75522246,2	K562	blood:
2	chr15:75504624..75507046-chr15:75507156..75508861,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261779	TF binding region
ENSG00000260660	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11072532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11072533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11072534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11072536	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11636245	0.85[CHB][hapmap]
rs11853027	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12591506	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12592411	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12708517	0.90[ASN][1000 genomes]
rs12904018	0.89[ASN][1000 genomes]
rs1532155	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2006683	0.83[ASN][1000 genomes]
rs3743210	0.95[ASN][1000 genomes]
rs3743211	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4886430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886431	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4886677	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7403344	0.94[ASN][1000 genomes]
rs8025431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8039284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8043432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs902482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv904384	chr15:75493823-75520378	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv569995	chr15:75493823-75537475	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv569996	chr15:75493823-75540491	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv904385	chr15:75493823-75546700	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
12	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75500000-75510200	Strong transcription	Fetal Intestine Small	intestine
2	chr15:75503400-75508800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:75504200-75511400	Weak transcription	Stomach Mucosa	stomach
4	chr15:75504800-75508400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75504800-75508800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:75504800-75515800	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:75505200-75508600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:75505600-75508600	Weak transcription	A549	lung
9	chr15:75505600-75508600	Weak transcription	Osteobl	bone
10	chr15:75505600-75509000	Weak transcription	HSMMtube	muscle
11	chr15:75505600-75511400	Weak transcription	Liver	Liver
12	chr15:75505800-75508400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:75505800-75509000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:75505800-75510400	Weak transcription	GM12878-XiMat	blood
15	chr15:75505800-75511000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:75505800-75511200	Weak transcription	Colonic Mucosa	Colon
17	chr15:75505800-75511400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:75505800-75511600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:75505800-75512200	Weak transcription	Aorta	Aorta
20	chr15:75505800-75521400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:75506000-75508400	Weak transcription	Thymus	Thymus
22	chr15:75506000-75508800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:75506000-75508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:75506000-75509600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:75506000-75511000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:75506000-75511000	Weak transcription	HepG2	liver
27	chr15:75506000-75513800	Weak transcription	Pancreas	Pancrea
28	chr15:75506200-75508800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:75506200-75509600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:75506200-75512000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:75506400-75508400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr15:75506400-75508800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr15:75506400-75509000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr15:75506400-75509800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:75506400-75511200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:75506400-75511800	Weak transcription	Left Ventricle	heart
37	chr15:75506600-75508800	Weak transcription	NHLF	lung
38	chr15:75506600-75512000	Weak transcription	Primary B cells from cord blood	blood
39	chr15:75506600-75512200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:75506600-75514600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:75506800-75510600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:75506800-75510800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr15:75506800-75511200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:75506800-75514800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:75506800-75518400	Weak transcription	Ovary	ovary
46	chr15:75507000-75508600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:75507000-75509000	Weak transcription	Dnd41	blood
48	chr15:75507000-75509800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:75507000-75509800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:75507000-75510000	Weak transcription	Fetal Intestine Large	intestine

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