Variant report

Variant	rs11746722
Chromosome Location	chr5:70883136-70883137
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	MYC	chr5:70882130-70883653	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
2	MYBL2	chr5:70881842-70883381	HepG2	liver:	n/a	n/a
3	TAF7	chr5:70883028-70883367	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFIC	chr5:70883047-70883672	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr5:70881980-70883895	HepG2	liver:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
6	POLR2A	chr5:70882830-70883446	A549	lung:	n/a	n/a
7	POLR2A	chr5:70882522-70883509	GM12878	blood:	n/a	n/a
8	POLR2A	chr5:70882198-70883597	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:70882589-70883561	MCF-7	breast:	n/a	n/a
10	POLR2A	chr5:70882433-70883823	GM12891	blood:	n/a	n/a
11	SMC3	chr5:70882795-70883689	Hela-S3	cervix:	n/a	n/a
12	MTA3	chr5:70882525-70883641	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr5:70882749-70883706	HCT-116	colon:	n/a	n/a
14	RELA	chr5:70882338-70883846	GM15510	blood:	n/a	n/a
15	PAX5	chr5:70882777-70883393	GM12878	blood:	n/a	n/a
16	SP1	chr5:70882806-70883263	GM12878	blood:	n/a	chr5:70883060-70883070 chr5:70883059-70883071 chr5:70883060-70883070 chr5:70883059-70883071
17	TCF7L2	chr5:70882671-70883295	PANC-1	pancreas:	n/a	n/a
18	CBX3	chr5:70882642-70883499	HCT-116	colon:	n/a	n/a
19	TBP	chr5:70882191-70883777	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:70882416-70883830	Hela-S3	cervix:	n/a	n/a
21	BHLHE40	chr5:70882158-70883641	K562	blood:	n/a	chr5:70883491-70883512
22	GTF2B	chr5:70882577-70883298	K562	blood:	n/a	n/a
23	POU2F2	chr5:70882462-70883376	GM12891	blood:	n/a	n/a
24	MYC	chr5:70882130-70883321	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
25	TAF1	chr5:70882318-70883393	K562	blood:	n/a	n/a
26	HCFC1	chr5:70882080-70883740	Hela-S3	cervix:	n/a	n/a
27	TAF1	chr5:70882532-70883504	HepG2	liver:	n/a	n/a
28	HEY1	chr5:70882118-70883859	K562	blood:	n/a	chr5:70883102-70883111
29	POLR2A	chr5:70882731-70883760	Hela-S3	cervix:	n/a	n/a
30	HEY1	chr5:70882180-70883365	K562	blood:	n/a	chr5:70883102-70883111
31	USF1	chr5:70882756-70883585	SK-N-SH	brain:	n/a	chr5:70883491-70883512
32	IRF1	chr5:70881660-70883313	K562	blood:	n/a	chr5:70883045-70883054 chr5:70883059-70883073 chr5:70882354-70882375 chr5:70882377-70882398
33	RELA	chr5:70882569-70883812	GM12891	blood:	n/a	n/a
34	ATF2	chr5:70882534-70883150	GM12878	blood:	n/a	n/a
35	ZBTB7A	chr5:70882491-70883279	K562	blood:	n/a	n/a
36	POLR2A	chr5:70882120-70883466	PANC-1	pancreas:	n/a	n/a
37	MAX	chr5:70882073-70883731	HepG2	liver:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
38	RELA	chr5:70882798-70883770	GM19193	blood:	n/a	n/a
39	RFX5	chr5:70882350-70883329	K562	blood:	n/a	n/a
40	POLR2A	chr5:70882722-70883564	Hela-S3	cervix:	n/a	n/a
41	PML	chr5:70882433-70883450	K562	blood:	n/a	chr5:70883130-70883138
42	MAX	chr5:70882491-70883479	HUVEC	blood vessel:	n/a	chr5:70883100-70883110
43	USF1	chr5:70882801-70883380	A549	lung:	n/a	n/a
44	USF1	chr5:70882861-70883306	A549	lung:	n/a	n/a
45	MYC	chr5:70882084-70883802	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
46	POLR2A	chr5:70882141-70883315	HepG2	liver:	n/a	n/a
47	ATF3	chr5:70882921-70883240	K562	blood:	n/a	n/a
48	SPI1	chr5:70883041-70883235	K562	blood:	n/a	n/a
49	SMARCB1	chr5:70882806-70883829	Hela-S3	cervix:	n/a	n/a
50	ZEB1	chr5:70883085-70883490	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:70883087-70883137	SKMC	muscle:	n/a
2	chr5:70883087-70883137	SAEC	small airway:	n/a
3	chr5:70883096-70883146	HEEpiC	esophagus:	n/a
4	chr5:70883096-70883146	LNCaP	prostate:	n/a
5	chr5:70883087-70883137	SK-N-SH	brain:	n/a
6	chr5:70883096-70883146	AG04450	lung:	fetal
7	chr5:70883106-70883156	HCM	heart:	n/a
8	chr5:70883096-70883146	NHBE	bronchial:	n/a
9	chr5:70883096-70883146	CMK	blood:	n/a
10	chr5:70883094-70883144	PANC-1	pancreas:	n/a
11	chr5:70883094-70883144	SK-N-SH	brain:	n/a
12	chr5:70883106-70883156	Hela-S3	cervix:	n/a
13	chr5:70883096-70883146	GM12892	blood:	n/a
14	chr5:70883094-70883144	BE2_C	brain:	n/a
15	chr5:70883094-70883144	A549	lung:	n/a
16	chr5:70883096-70883146	MCF10A-Er-Src	breast:	n/a
17	chr5:70883087-70883137	NH-A	brain:	n/a
18	chr5:70883106-70883156	Caco-2	colon:	n/a
19	chr5:70883106-70883156	HL-60	blood:	n/a
20	chr5:70883096-70883146	BJ	skin:	n/a
21	chr5:70883106-70883156	Jurkat	blood:	n/a
22	chr5:70883094-70883144	HIPEpiC	eye:	n/a
23	chr5:70883106-70883156	HRCEpiC	kidney:	n/a
24	chr5:70883106-70883156	ovcar-3	ovarian:	n/a
25	chr5:70883106-70883156	SK-N-SH_RA	brain:	n/a
26	chr5:70883096-70883146	GM12891	blood:	n/a
27	chr5:70883094-70883144	U87	brain:	n/a
28	chr5:70883094-70883144	K562	blood:	n/a
29	chr5:70883094-70883144	Hela-S3	cervix:	n/a
30	chr5:70883094-70883144	HNPCEpiC	eye:	n/a
31	chr5:70883096-70883146	A549	lung:	n/a
32	chr5:70883106-70883156	HEK293	kidney:	embryo
33	chr5:70883096-70883146	HPAEpiC	pulmonary alveolar:	n/a
34	chr5:70883096-70883146	AoSMC	blood vessel:	n/a
35	chr5:70883106-70883156	HIPEpiC	eye:	n/a
36	chr5:70883096-70883146	HL-60	blood:	n/a
37	chr5:70883096-70883146	SAEC	small airway:	n/a
38	chr5:70883096-70883146	HCF	heart:	n/a
39	chr5:70883096-70883146	ovcar-3	ovarian:	n/a
40	chr5:70883087-70883137	HRE	kidney:	n/a
41	chr5:70883094-70883144	HMEC	breast:	n/a
42	chr5:70883106-70883156	HRPEpiC	eye:	n/a
43	chr5:70883096-70883146	HRE	kidney:	n/a
44	chr5:70883096-70883146	HCPEpiC	choroid plexus:	n/a
45	chr5:70883094-70883144	HCM	heart:	n/a
46	chr5:70883094-70883144	MCF-7	breast:	n/a
47	chr5:70883096-70883146	MCF-7	breast:	n/a
48	chr5:70883087-70883137	HL-60	blood:	n/a
49	chr5:70883096-70883146	T-47D	breast:	n/a
50	chr5:70883087-70883137	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr5:70882161..70884487-chr5:70891024..70893721,4	MCF-7	breast:
2	chr5:70749978..70751854-chr5:70881938..70884932,2	K562	blood:
3	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
4	chr5:70882648..70886012-chr5:70920531..70924466,3	K562	blood:
5	chr5:70880665..70885311-chr5:70885640..70890340,6	K562	blood:
6	chr5:70880133..70886735-chr5:70895650..70901637,10	MCF-7	breast:
7	chr5:70881870..70884694-chr5:70885301..70891902,7	MCF-7	breast:
8	chr17:58754114..58755898-chr5:70882002..70883719,2	MCF-7	breast:
9	chr5:70882556..70884981-chr5:176924076..176925754,2	MCF-7	breast:

Variant related genes	Relation type
MCCC2	TF binding region
MCCC2	CpG island
ENSG00000131844	Chromatin interaction
ENSG00000145734	Chromatin interaction
ENSG00000196923	Chromatin interaction
ENSG00000141376	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10044572	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055460	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060578	0.85[EUR][1000 genomes]
rs10064099	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10077085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10434642	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10474383	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10805884	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10942284	0.85[EUR][1000 genomes]
rs10942533	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10942682	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942702	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743135	0.89[EUR][1000 genomes]
rs12152748	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12153571	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12514732	0.89[EUR][1000 genomes]
rs12516456	0.85[EUR][1000 genomes]
rs12652715	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13157835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748043	0.89[EUR][1000 genomes]
rs4062889	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4505929	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5005863	0.82[EUR][1000 genomes]
rs62361818	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6452722	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6452900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6453013	0.83[EUR][1000 genomes]
rs6453014	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453018	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453035	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453043	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6872235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6872671	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877289	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6877773	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6886336	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898471	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs715747	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7378662	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7380115	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7380280	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7444322	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7447726	0.85[EUR][1000 genomes]
rs7448422	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7449316	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7714527	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7715648	0.85[EUR][1000 genomes]
rs7721179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727576	0.85[EUR][1000 genomes]
rs7728577	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7735544	0.83[EUR][1000 genomes]
rs9968768	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats 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 target site	28 gene(s)	inside rSNPs	diseases
2	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11746722	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70881800-70883600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:70881800-70884200	Active TSS	K562	blood
3	chr5:70882000-70884000	Active TSS	Ovary	ovary
4	chr5:70882000-70884200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr5:70882000-70884200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:70882000-70884600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:70882200-70883400	Active TSS	Brain Substantia Nigra	brain
8	chr5:70882200-70883400	Active TSS	NHLF	lung
9	chr5:70882200-70883600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:70882200-70883600	Active TSS	Brain Hippocampus Middle	brain
11	chr5:70882200-70883600	Active TSS	Fetal Muscle Trunk	muscle
12	chr5:70882200-70883800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr5:70882200-70883800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:70882200-70883800	Bivalent/Poised TSS	HepG2	liver
15	chr5:70882200-70884000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr5:70882200-70884000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:70882200-70884000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:70882200-70884000	Active TSS	Left Ventricle	heart
19	chr5:70882200-70884200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:70882200-70884400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:70882200-70884400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr5:70882200-70884400	Active TSS	Right Atrium	heart
23	chr5:70882200-70884800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr5:70882200-70884800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:70882200-70885600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:70882400-70883400	Active TSS	NH-A	brain
27	chr5:70882400-70883600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:70882400-70883600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:70882400-70883600	Active TSS	Brain Germinal Matrix	brain
30	chr5:70882400-70883600	Active TSS	Colonic Mucosa	Colon
31	chr5:70882400-70883600	Active TSS	Fetal Brain Male	brain
32	chr5:70882400-70883600	Active TSS	Lung	lung
33	chr5:70882400-70883600	Active TSS	Thymus	Thymus
34	chr5:70882400-70883800	Active TSS	HSMMtube	muscle
35	chr5:70882400-70883800	Flanking Active TSS	HUVEC	blood vessel
36	chr5:70882400-70884000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:70882400-70884000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:70882400-70884000	Active TSS	Fetal Brain Female	brain
39	chr5:70882400-70884000	Active TSS	Psoas Muscle	Psoas
40	chr5:70882400-70884000	Active TSS	Right Ventricle	heart
41	chr5:70882400-70884000	Active TSS	HSMM	muscle
42	chr5:70882400-70884200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr5:70882400-70884400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr5:70882400-70884600	Active TSS	GM12878-XiMat	blood
45	chr5:70882600-70883200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:70882600-70883600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:70882600-70883600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:70882600-70883600	Active TSS	Esophagus	oesophagus
49	chr5:70882600-70883600	Active TSS	Fetal Stomach	stomach
50	chr5:70882600-70883800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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