Variant report

Variant	rs28530689
Chromosome Location	chr12:122500748-122500749
allele	A/C
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	FOXA2	chr12:122500664-122501430	A549	lung:	n/a	n/a
2	GABPA	chr12:122500689-122501657	A549	lung:	n/a	n/a
3	TCF12	chr12:122500478-122503084	A549	lung:	n/a	chr12:122501076-122501085
4	NR3C1	chr12:122500662-122501290	A549	lung:	n/a	n/a
5	POLR2A	chr12:122500717-122503319	PFSK-1	brain:	n/a	n/a
6	NR2F2	chr12:122500499-122502388	MCF-7	breast:	n/a	n/a
7	JUND	chr12:122500675-122501613	A549	lung:	n/a	chr12:122501405-122501413 chr12:122501406-122501417 chr12:122501403-122501415 chr12:122501405-122501412
8	GATA3	chr12:122500614-122501801	MCF-7	breast:	n/a	n/a
9	HDAC2	chr12:122500642-122502014	MCF-7	breast:	n/a	chr12:122501076-122501085
10	NR3C1	chr12:122500690-122501349	A549	lung:	n/a	n/a
11	NR2F2	chr12:122500579-122503676	K562	blood:	n/a	n/a
12	POLR2A	chr12:122500699-122502538	HUVEC	blood vessel:	n/a	n/a
13	REST	chr12:122500595-122501570	A549	lung:	n/a	chr12:122500899-122500912
14	GABPA	chr12:122500679-122501683	MCF-7	breast:	n/a	n/a
15	EP300	chr12:122500717-122501670	A549	lung:	n/a	chr12:122501076-122501086
16	POLR2A	chr12:122500680-122501880	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr12:122500659-122502534	MCF-7	breast:	n/a	chr12:122501211-122501221 chr12:122502164-122502174
18	POLR2A	chr12:122500556-122501673	HUVEC	blood vessel:	n/a	n/a
19	GATA3	chr12:122500665-122502283	MCF-7	breast:	n/a	n/a
20	HDAC2	chr12:122500717-122501553	HepG2	liver:	n/a	chr12:122501076-122501085
21	SIN3AK20	chr12:122500496-122502361	MCF-7	breast:	n/a	n/a
22	POLR2A	chr12:122500601-122501495	HUVEC	blood vessel:	n/a	n/a
23	HDAC2	chr12:122500646-122501744	MCF-7	breast:	n/a	chr12:122501076-122501085
24	SIN3AK20	chr12:122500590-122501224	SK-N-SH	brain:	n/a	n/a
25	BCL3	chr12:122500508-122502854	A549	lung:	n/a	n/a
26	MAX	chr12:122500593-122503213	HepG2	liver:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
27	BCL3	chr12:122500736-122501538	A549	lung:	n/a	n/a
28	POLR2A	chr12:122500701-122501590	MCF-7	breast:	n/a	n/a
29	E2F6	chr12:122500692-122502692	A549	lung:	n/a	chr12:122502213-122502224 chr12:122501177-122501188
30	KAP1	chr12:122500702-122501607	HEK293	kidney:	n/a	chr12:122501403-122501412
31	POLR2A	chr12:122500304-122503304	HepG2	liver:	n/a	n/a
32	MAX	chr12:122500579-122503228	A549	lung:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
33	NR2F2	chr12:122500663-122501755	MCF-7	breast:	n/a	n/a
34	MAX	chr12:122500544-122503204	HepG2	liver:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
35	POLR2A	chr12:122500398-122501590	SK-N-MC	brain:	n/a	n/a
36	FOXA2	chr12:122500588-122501592	A549	lung:	n/a	n/a
37	ELF1	chr12:122500748-122501749	MCF-7	breast:	n/a	n/a
38	POLR2A	chr12:122500490-122500944	K562	blood:	n/a	n/a
39	POLR2A	chr12:122500587-122502442	SK-N-SH	brain:	n/a	n/a
40	MAZ	chr12:122500595-122503584	IMR90	lung:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122503332-122503341
41	POLR2A	chr12:122500627-122503403	PFSK-1	brain:	n/a	n/a
42	REST	chr12:122500676-122501433	PFSK-1	brain:	n/a	chr12:122500899-122500912
43	SP1	chr12:122500566-122501612	A549	lung:	n/a	chr12:122500786-122500800 chr12:122500753-122500766
44	HEY1	chr12:122500686-122501606	HepG2	liver:	n/a	n/a
45	SRF	chr12:122500720-122501736	MCF-7	breast:	n/a	n/a
46	SP1	chr12:122500606-122501669	A549	lung:	n/a	chr12:122500786-122500800 chr12:122500753-122500766
47	MAX	chr12:122500693-122501641	A549	lung:	n/a	chr12:122501211-122501221
48	POLR2A	chr12:122500483-122503329	SK-N-SH	brain:	n/a	n/a
49	MAX	chr12:122500576-122503298	HCT-116	colon:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
50	POLR2A	chr12:122500734-122503476	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122237524..122241320-chr12:122500575..122503777,5	K562	blood:
2	chr12:122500561..122501161-chr12:122582495..122583250,2	MCF-7	breast:
3	chr12:122459539..122463256-chr12:122498402..122502892,4	MCF-7	breast:
4	chr12:122460064..122462817-chr12:122499395..122500991,2	MCF-7	breast:
5	chr12:122459811..122462052-chr12:122500619..122502679,2	K562	blood:
6	chr12:122499616..122503062-chr12:122514965..122517800,5	MCF-7	breast:
7	chr12:122499171..122504349-chr12:122514733..122520643,17	K562	blood:

Variant related genes	Relation type
ENSG00000256546	TF binding region
ENSG00000110987	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1047796	0.83[AMR][1000 genomes]
rs1047813	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10744177	0.81[EUR][1000 genomes]
rs10744335	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10770189	0.83[EUR][1000 genomes]
rs10773037	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10846525	0.82[AMR][1000 genomes]
rs11057184	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057654	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11057905	0.84[EUR][1000 genomes]
rs11059094	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11060477	0.91[EUR][1000 genomes]
rs11061156	0.87[EUR][1000 genomes]
rs11061602	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11608788	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11608792	0.91[EUR][1000 genomes]
rs11609875	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11835818	0.89[EUR][1000 genomes]
rs12366611	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12812519	0.84[EUR][1000 genomes]
rs1316787	0.80[EUR][1000 genomes]
rs1976859	0.86[EUR][1000 genomes]
rs2280573	0.86[EUR][1000 genomes]
rs2280574	0.87[EUR][1000 genomes]
rs28385906	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28401575	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28410367	0.87[EUR][1000 genomes]
rs28414202	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28421373	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28430881	0.92[EUR][1000 genomes]
rs28450064	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28453771	0.89[EUR][1000 genomes]
rs28461580	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28464252	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28478366	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28478717	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28498002	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28498376	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28503672	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28506952	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28517281	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28529535	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28545660	0.84[EUR][1000 genomes]
rs28548845	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28569273	0.90[EUR][1000 genomes]
rs28580546	0.87[EUR][1000 genomes]
rs28585613	0.90[EUR][1000 genomes]
rs28591322	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28605425	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28607028	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28613772	0.88[EUR][1000 genomes]
rs28626850	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28629903	0.89[EUR][1000 genomes]
rs28631172	0.89[EUR][1000 genomes]
rs28639626	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28642975	0.89[EUR][1000 genomes]
rs28649184	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28652632	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28683032	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28691281	0.88[EUR][1000 genomes]
rs28699616	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28737311	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28739522	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28759327	0.89[EUR][1000 genomes]
rs34047484	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34123446	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34532891	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34739240	0.82[EUR][1000 genomes]
rs34741056	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34974633	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35159488	0.83[EUR][1000 genomes]
rs35249105	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35676267	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35764187	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36079122	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809117	0.81[EUR][1000 genomes]
rs3892367	0.86[EUR][1000 genomes]
rs4758653	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4758654	0.80[EUR][1000 genomes]
rs4758685	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4758686	0.82[EUR][1000 genomes]
rs4758687	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4758690	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4758691	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61952902	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61952904	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61952920	0.93[EUR][1000 genomes]
rs61952922	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61952923	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6489238	0.83[EUR][1000 genomes]
rs6489242	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6489244	0.83[EUR][1000 genomes]
rs7137049	0.87[EUR][1000 genomes]
rs7312210	0.82[EUR][1000 genomes]
rs73217796	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7484733	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7485380	0.81[EUR][1000 genomes]
rs7485447	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7486198	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7488268	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7488393	0.84[EUR][1000 genomes]
rs7488857	0.82[EUR][1000 genomes]
rs7953704	0.82[EUR][1000 genomes]
rs7955571	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7955575	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7962500	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7964148	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7975001	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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	21 gene(s)	inside rSNPs	diseases
5	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:122472000-122507200	Weak transcription	Fetal Brain Male	brain
3	chr12:122475200-122501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:122491800-122501000	Strong transcription	Fetal Brain Female	brain
5	chr12:122492600-122505600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:122492800-122500800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr12:122492800-122501000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr12:122492800-122501600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:122493000-122500800	Strong transcription	Brain Germinal Matrix	brain
10	chr12:122497600-122501200	Weak transcription	Fetal Heart	heart
11	chr12:122497600-122502400	Enhancers	Ovary	ovary
12	chr12:122497800-122500800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:122498200-122501000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:122498400-122500800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:122498400-122500800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:122498400-122502400	Weak transcription	HSMMtube	muscle
17	chr12:122498800-122501000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:122498800-122501200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:122499200-122500800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:122499200-122500800	Weak transcription	Primary B cells from cord blood	blood
21	chr12:122499200-122501000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:122499400-122500800	Enhancers	Fetal Kidney	kidney
23	chr12:122499600-122501000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:122499600-122501000	Genic enhancers	Fetal Intestine Small	intestine
25	chr12:122499600-122501200	Enhancers	Colonic Mucosa	Colon
26	chr12:122499800-122500800	Enhancers	HUVEC	blood vessel
27	chr12:122500000-122500800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr12:122500000-122500800	Genic enhancers	Fetal Muscle Leg	muscle
29	chr12:122500000-122501200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:122500000-122501200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:122500000-122501400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:122500000-122501400	Enhancers	Placenta	Placenta
33	chr12:122500000-122501600	Genic enhancers	Thymus	Thymus
34	chr12:122500000-122501800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:122500000-122501800	Enhancers	HMEC	breast
36	chr12:122500000-122502200	Enhancers	Pancreas	Pancrea
37	chr12:122500000-122502600	Enhancers	Liver	Liver
38	chr12:122500000-122502600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr12:122500000-122503400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:122500000-122503600	Enhancers	Right Ventricle	heart
41	chr12:122500000-122504600	Enhancers	Stomach Mucosa	stomach
42	chr12:122500200-122500800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:122500200-122501000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:122500200-122501200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr12:122500200-122501200	Enhancers	Fetal Stomach	stomach
46	chr12:122500200-122501400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:122500200-122501400	Enhancers	Fetal Intestine Large	intestine
48	chr12:122500200-122501600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:122500200-122501800	Enhancers	NHEK	skin
50	chr12:122500200-122502200	Enhancers	NHDF-Ad	bronchial

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