Variant report

Variant	rs2160588
Chromosome Location	chr12:12487447-12487448
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	CTCF	chr12:12487380-12487530	HAc	cerebellar:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
2	RAD21	chr12:12487325-12487688	GM12878	blood:	n/a	chr12:12487468-12487477 chr12:12487501-12487520 chr12:12487505-12487519 chr12:12487509-12487522
3	CTCF	chr12:12487408-12487690	A549	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
4	CTCF	chr12:12487400-12487550	GM12875	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
5	MAX	chr12:12487294-12487666	Hela-S3	cervix:	n/a	n/a
6	MAX	chr12:12487366-12487674	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr12:12487360-12487510	HFF-Myc	foreskin:	n/a	n/a
8	CTCF	chr12:12487440-12487590	WERI-Rb-1	eye:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
9	MAX	chr12:12487315-12487684	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr12:12487386-12487589	K562	blood:	n/a	chr12:12487468-12487477 chr12:12487501-12487520 chr12:12487505-12487519 chr12:12487509-12487522
11	CTCF	chr12:12487366-12487667	Spleen_OC	spleen:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
12	CTCF	chr12:12487400-12487550	Caco-2	colon:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
13	CTCF	chr12:12487440-12487590	GM12869	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
14	CTCF	chr12:12487420-12487570	AG10803	skin:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
15	SIN3AK20	chr12:12487298-12487622	A549	lung:	n/a	n/a
16	CTCF	chr12:12487333-12487806	MCF-7	breast:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
17	CTCF	chr12:12487375-12487654	GM10266	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
18	CTCF	chr12:12487377-12487619	MCF-7	breast:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
19	CTCF	chr12:12487420-12487570	AG04450	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
20	CTCF	chr12:12487380-12487530	A549	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
21	CTCF	chr12:12487366-12487636	GM19238	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
22	CTCF	chr12:12487440-12487590	HL-60	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
23	CTCF	chr12:12487440-12487590	HEK293	kidney:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
24	RAD21	chr12:12487307-12487636	H1-hESC	embryonic stem cell:	n/a	chr12:12487468-12487477 chr12:12487501-12487520 chr12:12487505-12487519 chr12:12487509-12487522
25	ATF3	chr12:12487209-12487689	A549	lung:	n/a	n/a
26	CTCF	chr12:12487374-12487626	A549	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
27	CTCF	chr12:12487400-12487550	HCFaa	heart:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
28	CTCF	chr12:12487440-12487590	HUVEC	blood vessel:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
29	SMC3	chr12:12487313-12487687	K562	blood:	n/a	chr12:12487505-12487519 chr12:12487321-12487331 chr12:12487512-12487519
30	MAX	chr12:12487392-12487646	K562	blood:	n/a	n/a
31	CTCF	chr12:12487405-12487630	GM20000	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
32	CTCF	chr12:12487420-12487570	GM12871	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
33	CTCF	chr12:12487273-12487685	A549	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
34	ELF1	chr12:12487273-12487591	A549	lung:	n/a	n/a
35	CTCF	chr12:12487420-12487570	HBMEC	blood vessel:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
36	POU2F2	chr12:12487356-12487625	GM12891	blood:	n/a	chr12:12487431-12487443 chr12:12487432-12487442 chr12:12487431-12487444
37	MYC	chr12:12487334-12487645	MCF10A-Er-Src	breast:	n/a	n/a
38	MYC	chr12:12487294-12487614	K562	blood:	n/a	n/a
39	PBX3	chr12:12487386-12487544	GM12878	blood:	n/a	n/a
40	CTCF	chr12:12487420-12487570	HEEpiC	esophagus:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
41	CTCF	chr12:12487298-12487761	IMR90	lung:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
42	CTCF	chr12:12487420-12487570	GM12865	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
43	RAD21	chr12:12487252-12487756	MCF-7	breast:	n/a	chr12:12487468-12487477 chr12:12487501-12487520 chr12:12487505-12487519 chr12:12487509-12487522
44	YY1	chr12:12487333-12487657	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr12:12487440-12487590	HRPEpiC	eye:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
46	CTCF	chr12:12487420-12487570	AG09319	gingival:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
47	CTCF	chr12:12487420-12487570	BJ	skin:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
48	USF2	chr12:12487381-12487622	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr12:12487380-12487530	GM12873	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518
50	CTCF	chr12:12487420-12487570	GM12864	blood:	n/a	chr12:12487498-12487519 chr12:12487503-12487521 chr12:12487506-12487516 chr12:12487504-12487520 chr12:12487509-12487518

No.	Distal block	Cell Line	Cell type
1	chr12:12234847..12235643-chr12:12487037..12487905,2	MCF-7	breast:
2	chr12:12486786..12487683-chr12:12503028..12503718,2	K562	blood:
3	chr12:12419232..12421863-chr12:12485161..12488276,6	MCF-7	breast:
4	chr12:12234594..12235634-chr12:12486774..12487917,3	MCF-7	breast:
5	chr12:12487375..12490317-chr12:12509840..12512376,2	MCF-7	breast:
6	chr12:12234512..12235357-chr12:12487032..12487983,4	K562	blood:

Variant related genes	Relation type
ENSG00000243141	TF binding region
ENSG00000111261	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000070018	Chromatin interaction
ENSG00000205791	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17303178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372890	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3741798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55865572	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55892345	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56829405	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57725255	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922023	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922024	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922025	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922026	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922027	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61922044	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922045	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922046	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922047	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922049	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922052	0.96[ASN][1000 genomes]
rs61922054	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61922057	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73277486	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73277491	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73279305	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980482	1.00[CHB][hapmap];0.81[ASN][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898807	chr12:12448948-12502001	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2160588	LOH12CR1	cis	parietal	SCAN
rs2160588	KIAA1467	cis	cerebellum	SCAN
rs2160588	PRL	trans	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12473200-12501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:12473600-12493200	Weak transcription	Fetal Brain Female	brain
3	chr12:12473600-12502000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12473800-12487600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:12473800-12491800	Weak transcription	Left Ventricle	heart
6	chr12:12473800-12502400	Weak transcription	NHLF	lung
7	chr12:12474000-12489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:12477000-12487600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:12477200-12491800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:12480400-12490800	Weak transcription	Right Atrium	heart
11	chr12:12480400-12502400	Weak transcription	Right Ventricle	heart
12	chr12:12481200-12491000	Weak transcription	Hela-S3	cervix
13	chr12:12481200-12495400	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:12481200-12502200	Weak transcription	Fetal Heart	heart
15	chr12:12481800-12502400	Weak transcription	Psoas Muscle	Psoas
16	chr12:12482400-12502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:12483600-12487600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:12483600-12487600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:12483600-12488400	Enhancers	Stomach Mucosa	stomach
20	chr12:12483600-12502800	Weak transcription	Spleen	Spleen
21	chr12:12484200-12488200	Enhancers	Fetal Intestine Large	intestine
22	chr12:12484200-12488200	Enhancers	Fetal Lung	lung
23	chr12:12484600-12488200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:12484800-12487800	Weak transcription	Placenta	Placenta
25	chr12:12484800-12491800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:12485000-12487600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr12:12485200-12487600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:12485200-12488000	Enhancers	Fetal Thymus	thymus
29	chr12:12485200-12489200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:12485400-12489000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:12485400-12489200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:12485400-12489200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:12485400-12500200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:12485400-12502400	Weak transcription	Esophagus	oesophagus
35	chr12:12485400-12502800	Weak transcription	Gastric	stomach
36	chr12:12485400-12502800	Weak transcription	Small Intestine	intestine
37	chr12:12486200-12487600	Enhancers	Colonic Mucosa	Colon
38	chr12:12486200-12487800	Enhancers	Fetal Kidney	kidney
39	chr12:12486200-12488000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:12486200-12488000	Enhancers	Brain Hippocampus Middle	brain
41	chr12:12486200-12488200	Genic enhancers	HUVEC	blood vessel
42	chr12:12486400-12487800	Enhancers	Primary B cells from peripheral blood	blood
43	chr12:12486400-12487800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:12486400-12487800	Enhancers	Brain Anterior Caudate	brain
45	chr12:12486400-12487800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr12:12486400-12487800	Enhancers	Dnd41	blood
47	chr12:12486400-12488000	Enhancers	Primary T cells fromperipheralblood	blood
48	chr12:12486400-12488000	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:12486400-12488000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr12:12486400-12488000	Enhancers	Brain Cingulate Gyrus	brain

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