Variant report

Variant	rs643372
Chromosome Location	chr12:121022640-121022641
allele	C/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	chr12:121022116-121022836	A549	lung:	n/a	chr12:121022348-121022361
2	CTCF	chr12:121022244-121022713	K562	blood:	n/a	chr12:121022348-121022361
3	RAD21	chr12:121022387-121022659	HepG2	liver:	n/a	n/a
4	MAX	chr12:121022063-121022651	A549	lung:	n/a	chr12:121022320-121022330
5	RAD21	chr12:121022331-121022680	IMR90	lung:	n/a	chr12:121022348-121022362
6	CTCF	chr12:121022091-121022895	SK-N-SH	brain:	n/a	chr12:121022348-121022361
7	HCFC1	chr12:121022490-121022646	K562	blood:	n/a	n/a
8	ZNF384	chr12:121022385-121023023	K562	blood:	n/a	n/a
9	MAZ	chr12:121022319-121022665	K562	blood:	n/a	chr12:121022320-121022330
10	UBTF	chr12:121022325-121022691	K562	blood:	n/a	n/a
11	RAD21	chr12:121022354-121022682	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr12:121022178-121022767	K562	blood:	n/a	chr12:121022348-121022361
13	RAD21	chr12:121022030-121022848	SK-N-SH	brain:	n/a	chr12:121022348-121022362
14	RAD21	chr12:121022268-121022733	MCF-7	breast:	n/a	chr12:121022348-121022362
15	RAD21	chr12:121022153-121022924	HCT-116	colon:	n/a	chr12:121022348-121022362
16	CREB1	chr12:121022537-121022925	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr12:121022438-121022823	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:121022632-121022672	H1-hESC	embryonic stem cell:	n/a	n/a
19	MXI1	chr12:121022631-121022831	Hela-S3	cervix:	n/a	n/a
20	HMGN3	chr12:121022269-121022771	K562	blood:	n/a	n/a
21	RAD21	chr12:121022315-121022649	HepG2	liver:	n/a	chr12:121022348-121022362
22	RCOR1	chr12:121022308-121022694	K562	blood:	n/a	n/a
23	SMC3	chr12:121022339-121022652	K562	blood:	n/a	chr12:121022348-121022362
24	TCF12	chr12:121022573-121022859	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr12:121022322-121022644	K562	blood:	n/a	chr12:121022434-121022448 chr12:121022614-121022628 chr12:121022619-121022628
26	CCNT2	chr12:121022296-121022781	K562	blood:	n/a	chr12:121022668-121022677
27	RAD21	chr12:121022295-121022772	ECC-1	luminal epithelium:	n/a	chr12:121022348-121022362
28	GABPA	chr12:121022436-121022891	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF263	chr12:121022150-121022892	HEK293-T-REx	kidney:	n/a	n/a
30	SMC3	chr12:121022351-121022652	GM12878	blood:	n/a	n/a
31	FOXA2	chr12:121022019-121022643	A549	lung:	n/a	n/a
32	YY1	chr12:121022231-121022751	H1-hESC	embryonic stem cell:	n/a	chr12:121022646-121022657 chr12:121022434-121022448 chr12:121022614-121022628 chr12:121022313-121022327 chr12:121022619-121022628 chr12:121022648-121022662
33	RAD21	chr12:121022408-121022663	GM12878	blood:	n/a	n/a
34	YY1	chr12:121022213-121022698	HCT-116	colon:	n/a	chr12:121022646-121022657 chr12:121022434-121022448 chr12:121022614-121022628 chr12:121022313-121022327 chr12:121022619-121022628 chr12:121022648-121022662
35	MAX	chr12:121022219-121022669	K562	blood:	n/a	chr12:121022320-121022330
36	CHD2	chr12:121022315-121022681	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr12:121022268-121022724	MCF-7	breast:	n/a	chr12:121022348-121022361
38	TCF7L2	chr12:121022080-121022804	HCT-116	colon:	n/a	n/a
39	TCF12	chr12:121022615-121022820	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:121022202-121022921	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr12:121022339-121022841	Hela-S3	cervix:	n/a	n/a
42	GTF2F1	chr12:121022633-121022723	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMC3	chr12:121022252-121022843	Hela-S3	cervix:	n/a	chr12:121022348-121022362
44	RAD21	chr12:121022226-121022802	H1-hESC	embryonic stem cell:	n/a	chr12:121022348-121022362
45	ZEB1	chr12:121022330-121022731	GM12878	blood:	n/a	n/a
46	ZNF143	chr12:121022417-121022640	K562	blood:	n/a	n/a
47	MAX	chr12:121022424-121022648	NB4	blood:	n/a	n/a
48	POLR2A	chr12:121022215-121022875	HCT-116	colon:	n/a	n/a
49	YY1	chr12:121022221-121022683	K562	blood:	n/a	chr12:121022646-121022657 chr12:121022434-121022448 chr12:121022614-121022628 chr12:121022313-121022327 chr12:121022619-121022628 chr12:121022648-121022662
50	RCOR1	chr12:121022179-121022791	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121018818..121020507-chr12:121022267..121023983,3	K562	blood:
2	chr12:121017632..121023235-chr12:121123750..121127979,5	K562	blood:
3	chr12:121021974..121024111-chr12:121148529..121150037,2	MCF-7	breast:
4	chr12:121021284..121022852-chr12:121123778..121125938,2	MCF-7	breast:
5	chr12:121020419..121023213-chr12:121085697..121088719,3	MCF-7	breast:
6	chr12:121018584..121021388-chr12:121022313..121024823,2	MCF-7	breast:

Variant related genes	Relation type
POP5	TF binding region
ENSG00000157782	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000110917	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1048830	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1050187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10744752	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10774549	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10774551	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774553	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10774555	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774560	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774561	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10849753	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10849754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849757	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849758	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849759	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849766	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849767	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11065132	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065145	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065149	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065150	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065151	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11065154	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12309824	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12312613	0.86[EUR][1000 genomes]
rs12370495	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12371550	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12813930	0.87[ASN][1000 genomes]
rs12814055	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563333	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2138251	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2168319	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233676	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235217	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2235218	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2292681	0.90[YRI][hapmap]
rs2393590	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213565	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742052	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759394	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3759396	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3893104	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3916065	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4766966	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4766968	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4766969	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767897	0.83[ASN][1000 genomes]
rs4767902	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767903	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767904	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767905	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767906	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767910	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767911	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767912	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767914	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767916	0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509445	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516479	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523522	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524735	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs546417	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55848094	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56029862	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs579919	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs585510	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603574	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608724	0.90[YRI][hapmap]
rs651627	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655530	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs670568	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs687873	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136951	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71454645	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308053	0.81[ASN][1000 genomes]
rs7471	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7488320	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs787947	0.90[YRI][hapmap]
rs9040	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9788155	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9795621	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973944	chr12:121017088-121027122	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs643372	COQ5	cis	Esophagus Muscularis	GTEx
rs643372	COQ5	cis	Heart Left Ventricle	GTEx
rs643372	COQ5	cis	Skin Sun Exposed Lower leg	GTEx
rs643372	COQ5	Cis_1M	lymphoblastoid	RTeQTL
rs643372	COQ5	cis	Nerve Tibial	GTEx
rs643372	COQ5	cis	Artery Aorta	GTEx
rs643372	COQ5	cis	Artery Tibial	GTEx
rs643372	COQ5	cis	Muscle Skeletal	GTEx
rs643372	COQ5	cis	lung	GTEx
rs643372	COQ5	cis	Adipose Subcutaneous	GTEx
rs643372	COQ5	cis	Frontal Cortex	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121019600-121027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:121020800-121022800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:121021000-121022800	Active TSS	Brain Anterior Caudate	brain
4	chr12:121021000-121022800	Bivalent Enhancer	Fetal Brain Male	brain
5	chr12:121021000-121022800	Flanking Active TSS	GM12878-XiMat	blood
6	chr12:121021000-121023000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr12:121021000-121023000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:121021000-121023000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:121021200-121022800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:121021200-121022800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr12:121021200-121022800	Enhancers	Spleen	Spleen
12	chr12:121021200-121023000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr12:121021200-121023000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr12:121021200-121023000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr12:121021400-121022800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:121021400-121022800	Bivalent Enhancer	Fetal Thymus	thymus
17	chr12:121021400-121022800	Enhancers	Stomach Mucosa	stomach
18	chr12:121021400-121023000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:121021400-121023000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr12:121021400-121023000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr12:121021600-121022800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:121021600-121022800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
23	chr12:121021600-121022800	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:121021800-121022800	Enhancers	Primary B cells from cord blood	blood
25	chr12:121021800-121022800	Active TSS	K562	blood
26	chr12:121021800-121023000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:121021800-121023000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr12:121021800-121023000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:121021800-121023000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr12:121021800-121023000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:121021800-121023000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:121021800-121023000	Active TSS	Brain Hippocampus Middle	brain
33	chr12:121021800-121023000	Active TSS	Rectal Smooth Muscle	rectum
34	chr12:121022000-121022800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:121022000-121022800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:121022000-121022800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:121022000-121022800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:121022000-121022800	Active TSS	A549	lung
39	chr12:121022000-121022800	Active TSS	Hela-S3	cervix
40	chr12:121022000-121023000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:121022000-121023000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:121022000-121023000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:121022000-121023000	Enhancers	Lung	lung
44	chr12:121022200-121022800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:121022200-121022800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:121022200-121022800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:121022200-121022800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:121022200-121022800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:121022200-121022800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:121022200-121022800	Flanking Active TSS	Primary hematopoietic stem cells	blood

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