Variant report

Variant	rs61955587
Chromosome Location	chr12:122688256-122688257
allele	A/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	POLR2A	chr12:122687742-122689281	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr12:122687489-122689016	SK-N-SH	brain:	n/a	chr12:122688411-122688426
3	PAX5	chr12:122688178-122688612	GM12878	blood:	n/a	n/a
4	E2F6	chr12:122687757-122688605	A549	lung:	n/a	chr12:122688480-122688490 chr12:122688016-122688027
5	PAX5	chr12:122688165-122688635	GM12892	blood:	n/a	n/a
6	MXI1	chr12:122687720-122688682	IMR90	lung:	n/a	chr12:122688411-122688426
7	POLR2A	chr12:122687808-122688518	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr12:122687881-122688483	MCF-7	breast:	n/a	chr12:122688247-122688257
9	POLR2A	chr12:122687764-122688498	A549	lung:	n/a	n/a
10	EGR1	chr12:122687767-122688470	ECC-1	luminal epithelium:	n/a	chr12:122688201-122688211 chr12:122688202-122688213 chr12:122687955-122687969 chr12:122688250-122688261 chr12:122688247-122688257 chr12:122688201-122688214 chr12:122688200-122688214 chr12:122688248-122688263 chr12:122688201-122688214 chr12:122688202-122688211 chr12:122688249-122688262 chr12:122688201-122688214 chr12:122688022-122688033 chr12:122688200-122688215 chr12:122687989-122688003 chr12:122688201-122688214 chr12:122688021-122688034
11	POLR2A	chr12:122687823-122688539	MCF-7	breast:	n/a	n/a
12	EGR1	chr12:122687754-122688386	K562	blood:	n/a	chr12:122688201-122688211 chr12:122688202-122688213 chr12:122687955-122687969 chr12:122688250-122688261 chr12:122688247-122688257 chr12:122688201-122688214 chr12:122688200-122688214 chr12:122688248-122688263 chr12:122688201-122688214 chr12:122688202-122688211 chr12:122688249-122688262 chr12:122688201-122688214 chr12:122688022-122688033 chr12:122688200-122688215 chr12:122687989-122688003 chr12:122688201-122688214 chr12:122688021-122688034
13	POLR2A	chr12:122687894-122688443	ProgFib	skin:	n/a	n/a
14	PAX5	chr12:122688214-122688463	GM12891	blood:	n/a	n/a
15	MAX	chr12:122687673-122688732	A549	lung:	n/a	chr12:122688247-122688257
16	MAX	chr12:122687708-122688608	HepG2	liver:	n/a	chr12:122688247-122688257
17	SP1	chr12:122687728-122688268	A549	lung:	n/a	chr12:122688247-122688256 chr12:122688217-122688226 chr12:122688248-122688257 chr12:122688246-122688258 chr12:122688216-122688225 chr12:122688246-122688258 chr12:122688247-122688257 chr12:122688053-122688065 chr12:122688216-122688225 chr12:122688247-122688261 chr12:122688216-122688226 chr12:122688199-122688209 chr12:122688247-122688257
18	MAX	chr12:122687687-122688755	ECC-1	luminal epithelium:	n/a	chr12:122688247-122688257
19	MAX	chr12:122687687-122688668	K562	blood:	n/a	chr12:122688247-122688257
20	MAX	chr12:122687694-122688634	H1-hESC	embryonic stem cell:	n/a	chr12:122688247-122688257
21	PAX5	chr12:122688250-122688429	GM12878	blood:	n/a	n/a
22	EGR1	chr12:122687781-122688283	K562	blood:	n/a	chr12:122688201-122688211 chr12:122688202-122688213 chr12:122687955-122687969 chr12:122688250-122688261 chr12:122688247-122688257 chr12:122688201-122688214 chr12:122688200-122688214 chr12:122688248-122688263 chr12:122688201-122688214 chr12:122688202-122688211 chr12:122688249-122688262 chr12:122688201-122688214 chr12:122688022-122688033 chr12:122688200-122688215 chr12:122687989-122688003 chr12:122688201-122688214 chr12:122688021-122688034
23	MAX	chr12:122688189-122688446	K562	blood:	n/a	chr12:122688247-122688257
24	POLR2A	chr12:122687782-122688511	MCF-7	breast:	n/a	n/a
25	POLR2A	chr12:122687931-122688452	MCF10A-Er-Src	breast:	n/a	n/a
26	EP300	chr12:122687754-122688268	T-47D	breast:	n/a	n/a
27	MAZ	chr12:122687857-122688444	K562	blood:	n/a	chr12:122688247-122688257
28	CBX3	chr12:122688187-122688422	K562	blood:	n/a	n/a
29	EP300	chr12:122687814-122688298	T-47D	breast:	n/a	n/a
30	EGR1	chr12:122687725-122688395	ECC-1	luminal epithelium:	n/a	chr12:122688201-122688211 chr12:122688202-122688213 chr12:122687955-122687969 chr12:122688250-122688261 chr12:122688247-122688257 chr12:122688201-122688214 chr12:122688200-122688214 chr12:122688248-122688263 chr12:122688201-122688214 chr12:122688202-122688211 chr12:122688249-122688262 chr12:122688201-122688214 chr12:122688022-122688033 chr12:122688200-122688215 chr12:122687989-122688003 chr12:122688201-122688214 chr12:122688021-122688034
31	E2F6	chr12:122687720-122688502	H1-hESC	embryonic stem cell:	n/a	chr12:122688480-122688490 chr12:122688016-122688027
32	TAF1	chr12:122687761-122688579	ECC-1	luminal epithelium:	n/a	n/a
33	MAX	chr12:122687690-122688609	A549	lung:	n/a	chr12:122688247-122688257
34	PAX5	chr12:122688233-122688491	GM12892	blood:	n/a	n/a
35	POLR2A	chr12:122687705-122688325	PFSK-1	brain:	n/a	n/a
36	CCNT2	chr12:122687951-122688540	K562	blood:	n/a	n/a
37	TCF12	chr12:122687782-122688477	ECC-1	luminal epithelium:	n/a	n/a
38	MYC	chr12:122687613-122688422	A549	lung:	n/a	chr12:122688247-122688257
39	E2F6	chr12:122687529-122688660	A549	lung:	n/a	chr12:122688480-122688490 chr12:122688016-122688027
40	E2F6	chr12:122687791-122688609	K562	blood:	n/a	chr12:122688480-122688490 chr12:122688016-122688027
41	MAX	chr12:122687746-122688568	H1-hESC	embryonic stem cell:	n/a	chr12:122688247-122688257
42	MYC	chr12:122687805-122688449	MCF10A-Er-Src	breast:	n/a	chr12:122688247-122688257
43	POLR2A	chr12:122688231-122692085	A549	lung:	n/a	n/a
44	POLR2A	chr12:122687689-122688454	SK-N-MC	brain:	n/a	n/a
45	GABPA	chr12:122688234-122689022	H1-hESC	embryonic stem cell:	n/a	chr12:122688735-122688744 chr12:122688248-122688257
46	POLR2A	chr12:122688202-122689374	GM12878	blood:	n/a	n/a
47	HMGN3	chr12:122687857-122689034	K562	blood:	n/a	n/a
48	GATA3	chr12:122687544-122688462	A549	lung:	n/a	n/a
49	SIN3AK20	chr12:122687794-122688666	PANC-1	pancreas:	n/a	n/a
50	TCF3	chr12:122688143-122688493	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122688160..122690771-chr12:122750336..122752523,2	MCF-7	breast:
2	chr12:122686753..122691904-chr12:122708300..122712516,9	MCF-7	breast:
3	chr12:122459108..122461135-chr12:122685513..122688465,2	K562	blood:
4	chr12:122614284..122615813-chr12:122686761..122688798,2	MCF-7	breast:
5	chr12:122685663..122693033-chr12:122702446..122708793,8	K562	blood:
6	chr12:122684854..122691366-chr12:122708809..122712343,7	K562	blood:

Variant related genes	Relation type
B3GNT4	TF binding region
ENSG00000175727	Chromatin interaction
ENSG00000139719	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11061368	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11836373	0.81[EUR][1000 genomes]
rs12426902	0.85[EUR][1000 genomes]
rs2089887	0.82[AMR][1000 genomes]
rs35422129	0.81[EUR][1000 genomes]
rs60995900	0.81[EUR][1000 genomes]
rs61954363	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61954365	0.87[AMR][1000 genomes]
rs61954366	0.87[AMR][1000 genomes]
rs61954367	0.87[AMR][1000 genomes]
rs61954368	0.87[AMR][1000 genomes]
rs61954369	0.87[AMR][1000 genomes]
rs61954370	0.87[AMR][1000 genomes]
rs61954371	0.82[AMR][1000 genomes]
rs61954374	0.87[AMR][1000 genomes]
rs61954376	0.82[AMR][1000 genomes]
rs61954377	0.82[AMR][1000 genomes]
rs61954378	0.87[AMR][1000 genomes]
rs61954381	0.82[AMR][1000 genomes]
rs61954382	0.87[AMR][1000 genomes]
rs61954383	0.87[AMR][1000 genomes]
rs61954393	0.82[AMR][1000 genomes]
rs61954394	0.82[AMR][1000 genomes]
rs61955586	0.82[EUR][1000 genomes]
rs61955588	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61955589	0.87[AMR][1000 genomes]
rs7311354	0.82[AMR][1000 genomes]
rs7953290	0.87[AMR][1000 genomes]
rs7964780	0.87[AMR][1000 genomes]
rs7968764	0.87[AMR][1000 genomes]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv3363771	chr12:122687274-122690547	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122687400-122688600	Active TSS	Brain Hippocampus Middle	brain
2	chr12:122687400-122688600	Active TSS	K562	blood
3	chr12:122687400-122689200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:122687400-122689200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr12:122687400-122689600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:122687400-122690000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:122687600-122688400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:122687600-122688400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:122687600-122688400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:122687600-122688400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr12:122687600-122688400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr12:122687600-122688600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr12:122687600-122688600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:122687600-122688600	Active TSS	Brain Substantia Nigra	brain
15	chr12:122687600-122688600	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr12:122687600-122688600	Bivalent/Poised TSS	Psoas Muscle	Psoas
17	chr12:122687600-122688600	Active TSS	A549	lung
18	chr12:122687600-122688600	Bivalent/Poised TSS	HSMM	muscle
19	chr12:122687600-122688600	Bivalent/Poised TSS	NH-A	brain
20	chr12:122687600-122688600	Active TSS	NHLF	lung
21	chr12:122687600-122688800	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr12:122687600-122688800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:122687600-122689000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:122687600-122689000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:122687600-122689000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr12:122687600-122689000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr12:122687600-122689200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr12:122687600-122689200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:122687600-122689200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:122687600-122689200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr12:122687600-122689200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr12:122687600-122689200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:122687600-122689200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
34	chr12:122687600-122689200	Bivalent/Poised TSS	HepG2	liver
35	chr12:122687600-122689400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
36	chr12:122687600-122689400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr12:122687600-122689400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:122687800-122688400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:122687800-122688400	Active TSS	Gastric	stomach
40	chr12:122687800-122688400	Bivalent/Poised TSS	Left Ventricle	heart
41	chr12:122687800-122688400	Bivalent/Poised TSS	HUVEC	blood vessel
42	chr12:122687800-122688400	Bivalent/Poised TSS	NHDF-Ad	bronchial
43	chr12:122687800-122688600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:122687800-122688600	Flanking Active TSS	Liver	Liver
45	chr12:122687800-122688600	Active TSS	Brain Cingulate Gyrus	brain
46	chr12:122687800-122688600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:122687800-122688600	Flanking Active TSS	Lung	lung
48	chr12:122687800-122688600	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
49	chr12:122687800-122688800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:122687800-122688800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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