Variant report

Variant	rs28372857
Chromosome Location	chr15:75748381-75748382
allele	C/G
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	CHD2	chr15:75747810-75748644	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr15:75748131-75748972	A549	lung:	n/a	n/a
3	POLR2A	chr15:75748352-75748681	A549	lung:	n/a	n/a
4	SP4	chr15:75747919-75748573	H1-hESC	embryonic stem cell:	n/a	chr15:75748258-75748269 chr15:75748231-75748242 chr15:75748252-75748268 chr15:75748213-75748224 chr15:75748161-75748177 chr15:75748229-75748245
5	MAZ	chr15:75746056-75748764	K562	blood:	n/a	chr15:75746442-75746452 chr15:75747384-75747394
6	POLR2A	chr15:75747989-75748589	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr15:75747797-75748734	Raji	blood:	n/a	n/a
8	YY1	chr15:75747846-75748550	HepG2	liver:	n/a	chr15:75748218-75748227 chr15:75747927-75747941
9	CHD1	chr15:75742311-75749635	IMR90	lung:	n/a	chr15:75746254-75746264 chr15:75743636-75743646 chr15:75747775-75747785 chr15:75747345-75747355
10	POLR2A	chr15:75742468-75748864	SK-N-MC	brain:	n/a	n/a
11	CCNT2	chr15:75746192-75748470	K562	blood:	n/a	chr15:75746256-75746265 chr15:75747106-75747115 chr15:75747418-75747427
12	POLR2A	chr15:75747866-75748671	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:75748278-75748753	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75747905-75748679	GM18951	blood:	n/a	n/a
15	SIN3AK20	chr15:75746558-75748584	K562	blood:	n/a	n/a
16	TAF1	chr15:75748183-75748440	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr15:75747830-75748733	U87	brain:	n/a	n/a
18	RUNX3	chr15:75748264-75748786	GM12878	blood:	n/a	n/a
19	SIN3A	chr15:75745880-75748786	GM12878	blood:	n/a	chr15:75747562-75747575 chr15:75748111-75748119
20	POLR2A	chr15:75747913-75748743	GM19193	blood:	n/a	n/a
21	CHD2	chr15:75748302-75748720	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr15:75747671-75748584	SK-N-SH	brain:	n/a	n/a
23	POU2F2	chr15:75748323-75748796	GM12891	blood:	n/a	n/a
24	POLR2A	chr15:75747925-75748735	HepG2	liver:	n/a	n/a
25	REST	chr15:75747480-75748793	A549	lung:	n/a	n/a
26	POLR2A	chr15:75747840-75748580	SK-N-MC	brain:	n/a	n/a
27	HEY1	chr15:75744164-75748809	K562	blood:	n/a	chr15:75747923-75747938 chr15:75744695-75744710 chr15:75747087-75747102
28	POLR2A	chr15:75747870-75748742	K562	blood:	n/a	n/a
29	EGR1	chr15:75747992-75748537	K562	blood:	n/a	chr15:75748216-75748229 chr15:75748254-75748269 chr15:75748252-75748266
30	EP300	chr15:75748335-75748467	HepG2	liver:	n/a	n/a
31	SIN3AK20	chr15:75748338-75748549	HepG2	liver:	n/a	n/a
32	SP1	chr15:75747963-75748768	GM12878	blood:	n/a	chr15:75748258-75748269 chr15:75748231-75748243 chr15:75748231-75748243 chr15:75748231-75748242 chr15:75748213-75748224 chr15:75748232-75748246 chr15:75748232-75748241
33	ZNF143	chr15:75748070-75748706	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr15:75747844-75748391	ECC-1	luminal epithelium:	n/a	n/a
35	MAZ	chr15:75742325-75749787	IMR90	lung:	n/a	chr15:75746442-75746452 chr15:75743410-75743420 chr15:75745344-75745353 chr15:75747384-75747394 chr15:75743317-75743327 chr15:75743090-75743100
36	POLR2A	chr15:75747745-75748729	K562	blood:	n/a	n/a
37	JUND	chr15:75745972-75748543	A549	lung:	n/a	chr15:75746434-75746443 chr15:75746363-75746372 chr15:75746257-75746266
38	SMARCB1	chr15:75745341-75748747	Hela-S3	cervix:	n/a	n/a
39	SIN3AK20	chr15:75748195-75748730	A549	lung:	n/a	n/a
40	POLR2A	chr15:75747891-75748747	GM12892	blood:	n/a	n/a
41	POLR2A	chr15:75745999-75748733	H1-neurons	neurons:	n/a	n/a
42	ELF1	chr15:75747778-75748832	GM12878	blood:	n/a	chr15:75748214-75748226 chr15:75748218-75748227
43	POLR2A	chr15:75742610-75748755	K562	blood:	n/a	n/a
44	PML	chr15:75747697-75748470	K562	blood:	n/a	n/a
45	POLR2A	chr15:75747825-75748762	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr15:75747862-75748787	PBDE	blood:	n/a	n/a
47	SP1	chr15:75747723-75748951	A549	lung:	n/a	chr15:75748258-75748269 chr15:75748231-75748243 chr15:75747884-75747897 chr15:75748231-75748243 chr15:75748231-75748242 chr15:75748213-75748224 chr15:75748232-75748246 chr15:75748232-75748241
48	HEY1	chr15:75748369-75748613	HepG2	liver:	n/a	n/a
49	HMGN3	chr15:75746158-75748692	K562	blood:	n/a	n/a
50	POU2F2	chr15:75748252-75748831	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75745404..75749003-chr15:75939962..75944253,7	K562	blood:
2	chr15:75741578..75748624-chr15:75927989..75935113,20	K562	blood:
3	chr15:75657601..75665504-chr15:75739437..75749700,27	K562	blood:
4	chr15:75746940..75749418-chr15:75762942..75765472,2	K562	blood:
5	chr15:75746963..75748575-chr15:75762243..75764464,2	MCF-7	breast:
6	chr15:75744354..75750304-chr15:75868474..75873810,11	K562	blood:
7	chr15:75742140..75749687-chr15:75929409..75934974,27	MCF-7	breast:
8	chr15:75743503..75749103-chr15:75916446..75919686,11	K562	blood:
9	chr15:75658070..75664945-chr15:75741625..75749756,25	K562	blood:
10	chr15:75748094..75748764-chr20:36661581..36662411,2	NB4	blood:
11	chr15:75741578..75748579-chr15:75928515..75935579,16	K562	blood:
12	chr15:75660169..75660968-chr15:75748162..75749013,2	Hela-S3	cervix:
13	chr15:75747297..75750090-chr15:75917042..75918594,2	MCF-7	breast:
14	chr15:75747688..75748427-chr5:142783692..142784491,2	NB4	blood:
15	chr15:75745526..75749103-chr15:75915153..75919928,6	K562	blood:
16	chr15:75656095..75662590-chr15:75739456..75750037,27	MCF-7	breast:
17	chr15:75657484..75665083-chr15:75741604..75749517,41	MCF-7	breast:
18	chr15:75746665..75750304-chr15:75867936..75873114,8	K562	blood:
19	chr15:75747614..75748882-chr6:74230241..74231226,3	Hela-S3	cervix:

Variant related genes	Relation type
SIN3A	TF binding region
ENSG00000173548	Chromatin interaction
ENSG00000260235	Chromatin interaction
ENSG00000101413	Chromatin interaction
ENSG00000101407	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000169410	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000260206	Chromatin interaction
ENSG00000169371	Chromatin interaction
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12591076	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591309	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12591954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12592026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593870	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12594671	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886434	1.00[EUR][1000 genomes]
rs4886435	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886445	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886685	1.00[EUR][1000 genomes]
rs4886689	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886697	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886701	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032031	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8035510	1.00[EUR][1000 genomes]
rs8035796	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788768	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS 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	161 gene(s)	inside rSNPs	diseases
6	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
8	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	nsv827389	chr15:75741918-75749453	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
13	esv3436937	chr15:75745924-75748772	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75741600-75748800	Active TSS	Ovary	ovary
2	chr15:75741800-75749000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:75742000-75748800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:75742200-75748600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:75742200-75748600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:75742200-75748600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr15:75742200-75748600	Active TSS	A549	lung
8	chr15:75742200-75748800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:75742200-75748800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:75742200-75748800	Active TSS	Fetal Kidney	kidney
11	chr15:75742200-75748800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:75742200-75749000	Active TSS	Psoas Muscle	Psoas
13	chr15:75742400-75748600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:75742400-75748600	Active TSS	Left Ventricle	heart
15	chr15:75742400-75748600	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr15:75742400-75748800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:75742400-75748800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:75742400-75748800	Active TSS	Right Atrium	heart
19	chr15:75742400-75749000	Active TSS	Fetal Intestine Large	intestine
20	chr15:75742400-75749200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr15:75742600-75748600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:75742600-75748600	Active TSS	Colon Smooth Muscle	Colon
23	chr15:75742600-75748600	Active TSS	GM12878-XiMat	blood
24	chr15:75742600-75748800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:75742600-75748800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:75742600-75748800	Active TSS	Aorta	Aorta
27	chr15:75742600-75748800	Active TSS	Small Intestine	intestine
28	chr15:75742600-75749200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr15:75742600-75749200	Active TSS	Thymus	Thymus
30	chr15:75742800-75748800	Active TSS	Lung	lung
31	chr15:75743200-75748600	Active TSS	Gastric	stomach
32	chr15:75745600-75748400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:75745600-75748600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:75745600-75748600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr15:75745600-75748600	Active TSS	Fetal Lung	lung
36	chr15:75745600-75748600	Active TSS	NHDF-Ad	bronchial
37	chr15:75745600-75749000	Active TSS	Esophagus	oesophagus
38	chr15:75745800-75748400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:75745800-75748400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr15:75745800-75748600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:75745800-75748600	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr15:75745800-75748800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:75745800-75749000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr15:75745800-75749000	Active TSS	Right Ventricle	heart
45	chr15:75746000-75748400	Active TSS	Duodenum Mucosa	Duodenum
46	chr15:75746000-75748400	Active TSS	Fetal Muscle Trunk	muscle
47	chr15:75746000-75748400	Active TSS	HUVEC	blood vessel
48	chr15:75746000-75748600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:75746000-75748600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:75746000-75748600	Active TSS	Primary T killer memory cells from peripheral blood	blood

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