Variant report

Variant	rs7962569
Chromosome Location	chr12:48577013-48577014
allele	C/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	RAD21	chr12:48576842-48577099	HepG2	liver:	n/a	n/a
2	CTCF	chr12:48576808-48577100	NHEK	skin:	n/a	n/a
3	CREB1	chr12:48576749-48577802	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF143	chr12:48576882-48577470	GM12878	blood:	n/a	chr12:48577451-48577461
5	CTCF	chr12:48576900-48577050	GM12868	blood:	n/a	n/a
6	CTCF	chr12:48576940-48577090	NHEK	skin:	n/a	n/a
7	SIN3A	chr12:48576618-48579251	H1-hESC	embryonic stem cell:	n/a	chr12:48577451-48577460
8	CTCF	chr12:48576814-48577040	A549	lung:	n/a	n/a
9	CTCF	chr12:48576900-48577050	NHEK	skin:	n/a	n/a
10	CTCF	chr12:48576799-48577300	GM12892	blood:	n/a	n/a
11	CTCF	chr12:48576920-48577070	GM12870	blood:	n/a	n/a
12	CTCF	chr12:48576900-48577050	GM12864	blood:	n/a	n/a
13	CTCF	chr12:48576900-48577050	HBMEC	blood vessel:	n/a	n/a
14	YY1	chr12:48576829-48577599	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr12:48576940-48577090	GM12874	blood:	n/a	n/a
16	CTCF	chr12:48576880-48577038	GM20000	blood:	n/a	n/a
17	CTCF	chr12:48576800-48577307	GM12891	blood:	n/a	n/a
18	CTCF	chr12:48576728-48577155	K562	blood:	n/a	n/a
19	CTCF	chr12:48576940-48577090	GM12864	blood:	n/a	n/a
20	MXI1	chr12:48576924-48577538	H1-hESC	embryonic stem cell:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
21	CTCF	chr12:48576762-48577162	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr12:48576817-48577113	MCF-7	breast:	n/a	n/a
23	MAX	chr12:48576656-48577909	A549	lung:	n/a	chr12:48577349-48577358 chr12:48577345-48577354
24	SP1	chr12:48576764-48577569	A549	lung:	n/a	chr12:48577261-48577275 chr12:48577133-48577147
25	KAP1	chr12:48576800-48577640	HEK293	kidney:	n/a	n/a
26	RCOR1	chr12:48576771-48577701	K562	blood:	n/a	n/a
27	CTCF	chr12:48576900-48577050	A549	lung:	n/a	n/a
28	CTCF	chr12:48576812-48577195	Gliobla	brain:	n/a	n/a
29	TAF1	chr12:48576869-48577545	A549	lung:	n/a	n/a
30	CTCF	chr12:48576898-48577086	Medullo	brain:	n/a	n/a
31	CTCF	chr12:48576852-48577043	GM13977	blood:	n/a	n/a
32	RAD21	chr12:48576798-48577102	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr12:48576838-48577090	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr12:48576721-48577073	HepG2	liver:	n/a	n/a
35	CTCF	chr12:48576880-48577030	HCFaa	heart:	n/a	n/a
36	MAZ	chr12:48576804-48577646	K562	blood:	n/a	chr12:48577349-48577358 chr12:48577345-48577354
37	CTCF	chr12:48576915-48577047	Pancreas_OC	pancreas:	n/a	n/a
38	HDAC2	chr12:48576728-48577846	MCF-7	breast:	n/a	chr12:48577529-48577538
39	ZBTB7A	chr12:48576991-48577778	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr12:48576920-48577070	BJ	skin:	n/a	n/a
41	CTCF	chr12:48576817-48577083	GM12878	blood:	n/a	n/a
42	TAF1	chr12:48576730-48577448	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:48576884-48577782	U87	brain:	n/a	n/a
44	CTCF	chr12:48576880-48577030	AG10803	skin:	n/a	n/a
45	CEBPB	chr12:48576862-48577501	H1-hESC	embryonic stem cell:	n/a	n/a
46	RCOR1	chr12:48576872-48577554	K562	blood:	n/a	n/a
47	TBP	chr12:48576647-48577475	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr12:48576795-48577660	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr12:48576804-48577158	A549	lung:	n/a	n/a
50	RAD21	chr12:48576842-48577030	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48548408..48551386-chr12:48576630..48579457,3	K562	blood:
2	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:

Variant related genes	Relation type
C12orf68	TF binding region
ASB8	TF binding region
ENSG00000269514	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1049392	0.89[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs10747529	0.94[JPT][hapmap]
rs10783235	0.92[MKK][hapmap]
rs10875733	0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs10875739	0.94[JPT][hapmap]
rs10875752	0.81[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875754	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10875759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875761	1.00[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875765	0.98[ASN][1000 genomes]
rs10875766	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11168350	0.87[JPT][hapmap]
rs11168353	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs11168354	0.94[JPT][hapmap]
rs11168358	0.94[JPT][hapmap]
rs11168363	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs11168364	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs11168373	0.93[JPT][hapmap]
rs11168404	0.81[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap]
rs11168417	0.89[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap]
rs11168424	0.89[CHB][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs11168434	0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168435	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168438	0.91[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11168439	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168442	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168443	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168444	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168445	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168448	0.81[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168453	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168454	0.90[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12228924	0.91[GIH][hapmap]
rs12422355	0.94[JPT][hapmap]
rs12423250	0.87[JPT][hapmap]
rs12425679	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17122567	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs1859443	0.87[JPT][hapmap]
rs1978161	0.88[JPT][hapmap]
rs2171643	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2286020	0.89[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2408954	0.94[JPT][hapmap]
rs3742075	0.86[JPT][hapmap]
rs3825403	0.94[JPT][hapmap]
rs4258439	0.94[JPT][hapmap]
rs56097189	0.96[ASN][1000 genomes]
rs57430775	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58540891	0.88[AMR][1000 genomes]
rs58556309	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59537300	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580658	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66507954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132898	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7133274	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136243	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136782	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136788	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299704	0.94[JPT][hapmap]
rs7302354	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7303677	0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs73104071	0.88[AMR][1000 genomes]
rs73105950	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73304926	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7484942	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs765260	0.94[JPT][hapmap]
rs7962390	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181670	1.00[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs886589	0.94[JPT][hapmap]
rs954326	0.87[JPT][hapmap]
rs9651981	0.91[GIH][hapmap];0.87[JPT][hapmap]
rs9804751	0.92[GIH][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7962569	C12orf41	cis	parietal	SCAN
rs7962569	C12orf68	cis	Esophagus Mucosa	GTEx
rs7962569	SNORA2B	cis	parietal	SCAN
rs7962569	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576200-48577200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:48576200-48577200	Flanking Active TSS	HMEC	breast
3	chr12:48576200-48577200	Flanking Bivalent TSS/Enh	NHEK	skin
4	chr12:48576200-48577400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:48576200-48578000	Active TSS	Brain Anterior Caudate	brain
6	chr12:48576200-48578000	Active TSS	Right Atrium	heart
7	chr12:48576200-48578200	Active TSS	Aorta	Aorta
8	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:48576200-48578600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:48576200-48579000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:48576200-48579000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
13	chr12:48576400-48577200	Flanking Active TSS	Ovary	ovary
14	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
15	chr12:48576400-48577200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr12:48576400-48577400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:48576400-48577400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
18	chr12:48576400-48577400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
19	chr12:48576400-48577400	Flanking Bivalent TSS/Enh	Dnd41	blood
20	chr12:48576400-48577600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr12:48576400-48577800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:48576400-48577800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
23	chr12:48576400-48577800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr12:48576400-48577800	Active TSS	NHLF	lung
25	chr12:48576400-48577800	Bivalent/Poised TSS	Osteobl	bone
26	chr12:48576400-48578000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chr12:48576400-48578800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
28	chr12:48576400-48578800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
29	chr12:48576600-48577200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
30	chr12:48576600-48577200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:48576600-48577200	Flanking Bivalent TSS/Enh	Fetal Heart	heart
32	chr12:48576600-48577200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
33	chr12:48576600-48577200	Flanking Active TSS	HUVEC	blood vessel
34	chr12:48576600-48577400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:48576600-48577400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:48576600-48577400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:48576600-48577400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:48576600-48577600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:48576600-48577600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
40	chr12:48576600-48577600	Flanking Active TSS	Placenta	Placenta
41	chr12:48576600-48577600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
42	chr12:48576600-48577800	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr12:48576600-48577800	Active TSS	Brain Hippocampus Middle	brain
44	chr12:48576600-48577800	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr12:48576600-48577800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
46	chr12:48576600-48577800	Flanking Active TSS	Right Ventricle	heart
47	chr12:48576600-48577800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
48	chr12:48576600-48578000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:48576600-48578000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:48576600-48578000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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