Variant report

Variant	rs28546198
Chromosome Location	chr7:112579355-112579356
allele	A/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	REST	chr7:112579189-112579580	ECC-1	luminal epithelium:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
2	CHD1	chr7:112579250-112579700	H1-hESC	embryonic stem cell:	n/a	chr7:112579459-112579469
3	MXI1	chr7:112578922-112580907	GM12878	blood:	n/a	n/a
4	TBP	chr7:112579274-112580745	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr7:112579255-112579453	GM12878	blood:	n/a	chr7:112579367-112579377 chr7:112579365-112579379
6	REST	chr7:112579022-112579760	H1-hESC	embryonic stem cell:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
7	POLR2A	chr7:112579349-112580919	GM18505	blood:	n/a	n/a
8	MAZ	chr7:112579008-112580815	K562	blood:	n/a	n/a
9	REST	chr7:112579196-112579527	HepG2	liver:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
10	POLR2A	chr7:112579150-112580782	K562	blood:	n/a	n/a
11	NRF1	chr7:112578593-112580941	SK-N-SH	brain:	n/a	chr7:112580161-112580175 chr7:112580161-112580172 chr7:112579458-112579467 chr7:112580160-112580171 chr7:112580206-112580217 chr7:112580161-112580170 chr7:112580158-112580172 chr7:112580208-112580217
12	JUND	chr7:112579316-112579425	H1-hESC	embryonic stem cell:	n/a	chr7:112579409-112579418
13	POLR2A	chr7:112578906-112580606	IMR90	lung:	n/a	n/a
14	MAZ	chr7:112579066-112580611	HepG2	liver:	n/a	n/a
15	MXI1	chr7:112578142-112581365	SK-N-SH	brain:	n/a	chr7:112578237-112578252 chr7:112578239-112578254
16	MXI1	chr7:112578757-112580531	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr7:112579274-112579457	GM12878	blood:	n/a	chr7:112579367-112579377 chr7:112579365-112579379
18	YY1	chr7:112579287-112580048	SK-N-SH_RA	brain:	n/a	chr7:112579522-112579533 chr7:112580021-112580035 chr7:112579458-112579467
19	REST	chr7:112579165-112579552	SK-N-SH	brain:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
20	SIN3AK20	chr7:112578969-112580805	MCF-7	breast:	n/a	n/a
21	RAD21	chr7:112579111-112579851	IMR90	lung:	n/a	chr7:112579516-112579530
22	WRNIP1	chr7:112579053-112579372	GM12878	blood:	n/a	n/a
23	REST	chr7:112579005-112580712	HL-60	blood:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
24	MTA3	chr7:112578909-112579658	GM12878	blood:	n/a	n/a
25	MYC	chr7:112578891-112580869	K562	blood:	n/a	n/a
26	JUND	chr7:112578842-112579785	H1-hESC	embryonic stem cell:	n/a	chr7:112579409-112579418
27	MAZ	chr7:112579043-112580682	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:112579343-112580640	GM18526	blood:	n/a	n/a
29	YY1	chr7:112579272-112579879	H1-hESC	embryonic stem cell:	n/a	chr7:112579522-112579533 chr7:112579458-112579467
30	SIN3A	chr7:112578914-112580696	H1-hESC	embryonic stem cell:	n/a	chr7:112579522-112579533 chr7:112579507-112579520 chr7:112580164-112580173
31	REST	chr7:112579267-112579504	Hela-S3	cervix:	n/a	chr7:112579367-112579377 chr7:112579365-112579379
32	ZNF263	chr7:112579174-112580916	HEK293-T-REx	kidney:	n/a	chr7:112579617-112579626 chr7:112579464-112579473
33	TAF1	chr7:112579286-112580998	H1-hESC	embryonic stem cell:	n/a	n/a
34	REST	chr7:112579023-112579616	GM12878	blood:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
35	MAX	chr7:112578952-112580739	K562	blood:	n/a	n/a
36	ELF1	chr7:112579298-112580254	GM12878	blood:	n/a	chr7:112580030-112580039
37	ZBTB7A	chr7:112579069-112580089	ECC-1	luminal epithelium:	n/a	n/a
38	CCNT2	chr7:112579172-112580391	K562	blood:	n/a	chr7:112579458-112579467 chr7:112579397-112579406
39	YY1	chr7:112579296-112580047	SK-N-SH_RA	brain:	n/a	chr7:112579522-112579533 chr7:112580021-112580035 chr7:112579458-112579467
40	REST	chr7:112579193-112579501	PFSK-1	brain:	n/a	chr7:112579367-112579377 chr7:112579365-112579379
41	MAX	chr7:112579060-112580556	K562	blood:	n/a	n/a
42	REST	chr7:112578949-112579663	H1-hESC	embryonic stem cell:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
43	GABPA	chr7:112579273-112580406	MCF-7	breast:	n/a	chr7:112580161-112580175 chr7:112580161-112580172 chr7:112579458-112579467 chr7:112580161-112580170 chr7:112580158-112580172 chr7:112580208-112580217
44	GABPA	chr7:112579345-112580394	K562	blood:	n/a	chr7:112580161-112580175 chr7:112580161-112580172 chr7:112579458-112579467 chr7:112580161-112580170 chr7:112580158-112580172 chr7:112580208-112580217
45	SIN3A	chr7:112579317-112580542	GM12878	blood:	n/a	chr7:112579522-112579533 chr7:112579507-112579520 chr7:112580164-112580173
46	POLR2A	chr7:112579013-112580635	H1-neurons	neurons:	n/a	n/a
47	REST	chr7:112578850-112579960	K562	blood:	n/a	chr7:112579367-112579377 chr7:112579507-112579520 chr7:112579365-112579379
48	TAF1	chr7:112579031-112580711	H1-neurons	neurons:	n/a	n/a
49	ZBTB7A	chr7:112579251-112580225	K562	blood:	n/a	n/a
50	CHD2	chr7:112579214-112580775	GM12878	blood:	n/a	chr7:112579459-112579469

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112428924..112430644-chr7:112579193..112581843,2	K562	blood:

Variant related genes	Relation type
C7orf60	TF binding region
ENSG00000146802	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10228144	1.00[ASN][1000 genomes]
rs10229725	1.00[ASN][1000 genomes]
rs10232962	1.00[ASN][1000 genomes]
rs10265199	1.00[ASN][1000 genomes]
rs10268162	1.00[ASN][1000 genomes]
rs10500013	0.86[EUR][1000 genomes]
rs12112310	1.00[ASN][1000 genomes]
rs17160084	1.00[ASN][1000 genomes]
rs1868588	1.00[ASN][1000 genomes]
rs2060636	1.00[ASN][1000 genomes]
rs28560010	1.00[ASN][1000 genomes]
rs28584529	1.00[ASN][1000 genomes]
rs28603026	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28624855	1.00[ASN][1000 genomes]
rs28722087	1.00[ASN][1000 genomes]
rs6964755	1.00[ASN][1000 genomes]
rs6968845	1.00[ASN][1000 genomes]
rs6973297	1.00[ASN][1000 genomes]
rs73196918	1.00[ASN][1000 genomes]
rs7341402	1.00[ASN][1000 genomes]
rs73718127	1.00[ASN][1000 genomes]
rs73718130	1.00[ASN][1000 genomes]
rs73718137	1.00[ASN][1000 genomes]
rs7777041	1.00[ASN][1000 genomes]
rs7798366	1.00[ASN][1000 genomes]
rs7800661	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3692941	chr7:112571420-112614215	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription 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	2 gene(s)	inside rSNPs	n/a
7	esv1795316	chr7:112577657-112588734	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1027981	chr7:112577657-112613212	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112551600-112579400	Weak transcription	Spleen	Spleen
2	chr7:112576800-112580800	Active TSS	Left Ventricle	heart
3	chr7:112577400-112580800	Active TSS	Right Ventricle	heart
4	chr7:112577600-112580200	Active TSS	Right Atrium	heart
5	chr7:112577600-112580600	Active TSS	Brain Angular Gyrus	brain
6	chr7:112577600-112580800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:112577600-112581000	Active TSS	Fetal Brain Female	brain
8	chr7:112577600-112581400	Active TSS	Aorta	Aorta
9	chr7:112577800-112580600	Active TSS	HSMMtube	muscle
10	chr7:112578000-112580600	Active TSS	Brain Anterior Caudate	brain
11	chr7:112578000-112580600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr7:112578000-112580800	Active TSS	NHLF	lung
13	chr7:112578000-112581000	Active TSS	Brain Germinal Matrix	brain
14	chr7:112578200-112579400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr7:112578200-112579400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr7:112578200-112579400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr7:112578200-112580400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:112578200-112580600	Active TSS	Fetal Heart	heart
19	chr7:112578200-112580800	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr7:112578200-112581000	Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:112578400-112580400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:112578400-112580400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:112578400-112580400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:112578400-112580400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:112578400-112580400	Active TSS	Fetal Stomach	stomach
26	chr7:112578400-112580400	Active TSS	GM12878-XiMat	blood
27	chr7:112578400-112580600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:112578400-112580600	Active TSS	Fetal Intestine Large	intestine
29	chr7:112578400-112580600	Active TSS	Fetal Intestine Small	intestine
30	chr7:112578400-112580800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:112578400-112581000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:112578600-112579400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:112578600-112579400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr7:112578600-112579600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr7:112578600-112579800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr7:112578600-112580200	Active TSS	HepG2	liver
37	chr7:112578600-112580400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:112578600-112580400	Active TSS	Fetal Kidney	kidney
39	chr7:112578600-112580600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:112578600-112580600	Active TSS	Fetal Brain Male	brain
41	chr7:112578600-112580800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr7:112578600-112580800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:112578600-112580800	Active TSS	Ovary	ovary
44	chr7:112578600-112581000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr7:112578600-112581000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:112578600-112581000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:112578600-112581000	Active TSS	Colonic Mucosa	Colon
48	chr7:112578600-112581000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr7:112578600-112581000	Active TSS	A549	lung
50	chr7:112578600-112581200	Active TSS	ES-I3 Cell Line	embryonic stem cell

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