Variant report

Variant	rs28431122
Chromosome Location	chr15:75505853-75505854
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	POLR2A	chr15:75505692-75505953	HepG2	liver:	n/a	n/a
2	BCLAF1	chr15:75505652-75508826	GM12878	blood:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
3	POLR2A	chr15:75505563-75508929	ECC-1	luminal epithelium:	n/a	n/a
4	BCLAF1	chr15:75504465-75508533	GM12878	blood:	n/a	chr15:75504683-75504692 chr15:75507383-75507390 chr15:75507561-75507574
5	POLR2A	chr15:75503968-75508962	GM18526	blood:	n/a	n/a
6	POLR2A	chr15:75503585-75508807	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:75505567-75505953	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:75505246-75506621	HEK293	kidney:	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	chr15:75504973-75507965	NB4	blood:	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	POLR2A	chr15:75505569-75505981	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr15:75505644-75505958	K562	blood:	n/a	n/a
16	POLR2A	chr15:75504559-75509010	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr15:75504349-75506939	K562	blood:	n/a	n/a
18	POLR2A	chr15:75499212-75509025	GM12892	blood:	n/a	n/a
19	POLR2A	chr15:75503799-75508816	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:75501382-75508952	Hela-S3	cervix:	n/a	n/a
21	ATF2	chr15:75505713-75508426	GM12878	blood:	n/a	n/a
22	FOSL2	chr15:75504754-75508851	HepG2	liver:	n/a	chr15:75506822-75506831
23	POLR2A	chr15:75499180-75510106	GM12892	blood:	n/a	n/a
24	POLR2A	chr15:75504543-75505953	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:75503447-75508620	K562	blood:	n/a	n/a
26	RXRA	chr15:75505014-75507308	GM12878	blood:	n/a	chr15:75506267-75506278 chr15:75506625-75506634
27	POLR2A	chr15:75505335-75508435	HCT-116	colon:	n/a	n/a
28	NFATC1	chr15:75504997-75509017	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:75505751-75506546	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:75505533-75507243	PANC-1	pancreas:	n/a	n/a
31	BCL3	chr15:75505663-75508535	A549	lung:	n/a	chr15:75507383-75507390 chr15:75507561-75507574
32	POLR2A	chr15:75505533-75505973	A549	lung:	n/a	n/a
33	POLR2A	chr15:75503536-75507041	K562	blood:	n/a	n/a
34	POU2F2	chr15:75504331-75508597	GM12891	blood:	n/a	chr15:75506170-75506182 chr15:75506167-75506179
35	POLR2A	chr15:75503496-75508425	HepG2	liver:	n/a	n/a
36	POLR2A	chr15:75503181-75509014	GM12892	blood:	n/a	n/a
37	ATF2	chr15:75505238-75505864	GM12878	blood:	n/a	n/a
38	ELF1	chr15:75505337-75506053	GM12878	blood:	n/a	chr15:75505566-75505578
39	POLR2A	chr15:75504935-75508761	PFSK-1	brain:	n/a	n/a
40	FOXM1	chr15:75505379-75507493	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:75504321-75508791	GM12891	blood:	n/a	n/a
42	POLR2A	chr15:75503737-75510069	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:75504821-75509048	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr15:75505325-75506768	H1-hESC	embryonic stem cell:	n/a	n/a
45	PML	chr15:75505543-75505976	GM12878	blood:	n/a	chr15:75505802-75505810
46	POLR2A	chr15:75503618-75508948	HL-60	blood:	n/a	n/a
47	POLR2A	chr15:75499185-75510301	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:75503743-75508848	K562	blood:	n/a	n/a
49	POLR2A	chr15:75505652-75506534	SK-N-MC	brain:	n/a	n/a
50	PML	chr15:75504134-75508939	GM12878	blood:	n/a	chr15:75505802-75505810 chr15:75508800-75508809

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75315929..75318210-chr15:75504654..75506646,2	MCF-7	breast:
2	chr15:75504624..75507046-chr15:75507156..75508861,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261779	TF binding region
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11072532	1.00[EUR][1000 genomes]
rs11072533	1.00[EUR][1000 genomes]
rs12591506	1.00[EUR][1000 genomes]
rs28528682	0.91[AFR][1000 genomes]
rs3743210	1.00[EUR][1000 genomes]
rs58508832	0.83[ASN][1000 genomes]
rs73437050	1.00[ASN][1000 genomes]
rs73437064	1.00[ASN][1000 genomes]
rs73437077	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7403344	1.00[EUR][1000 genomes]
rs8042034	1.00[EUR][1000 genomes];1.00[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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75496200-75506000	Weak transcription	Fetal Brain Female	brain
2	chr15:75496400-75506000	Weak transcription	Psoas Muscle	Psoas
3	chr15:75496600-75506600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:75496800-75507200	Weak transcription	NH-A	brain
5	chr15:75497600-75507000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:75497800-75506400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:75498000-75506000	Strong transcription	Thymus	Thymus
8	chr15:75498000-75507000	Genic enhancers	Spleen	Spleen
9	chr15:75498200-75506000	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr15:75498200-75506200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:75498200-75506200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:75498200-75507000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:75498200-75508000	Strong transcription	Fetal Stomach	stomach
14	chr15:75498400-75506600	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr15:75498400-75506600	Strong transcription	NHLF	lung
16	chr15:75498400-75507000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:75498400-75507000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:75498400-75507200	Strong transcription	Primary T cells from cord blood	blood
19	chr15:75498400-75507200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:75498600-75506000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:75500000-75507000	Strong transcription	Fetal Intestine Large	intestine
22	chr15:75500000-75510200	Strong transcription	Fetal Intestine Small	intestine
23	chr15:75500800-75507000	Strong transcription	Dnd41	blood
24	chr15:75501000-75506800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr15:75501200-75506000	Weak transcription	Right Atrium	heart
26	chr15:75501800-75506400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:75502000-75506000	Strong transcription	HepG2	liver
28	chr15:75502000-75506400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:75502000-75507000	Strong transcription	Gastric	stomach
30	chr15:75502200-75507600	Weak transcription	Fetal Heart	heart
31	chr15:75502400-75506000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75502400-75507000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:75502600-75506200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:75502800-75506800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:75503000-75507800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:75503200-75507400	Strong transcription	Placenta	Placenta
37	chr15:75503400-75506000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:75503400-75506400	Strong transcription	Fetal Thymus	thymus
39	chr15:75503400-75506800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr15:75503400-75507200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:75503400-75508800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:75503600-75506000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:75503600-75506200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:75503600-75507400	Strong transcription	Lung	lung
45	chr15:75503800-75506000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:75503800-75506600	Strong transcription	Primary B cells from cord blood	blood
47	chr15:75504000-75506400	Weak transcription	Brain Substantia Nigra	brain
48	chr15:75504000-75506600	Weak transcription	NHDF-Ad	bronchial
49	chr15:75504200-75506000	Strong transcription	Pancreas	Pancrea
50	chr15:75504200-75506200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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