Variant report

Variant	rs3741605
Chromosome Location	chr12:66696255-66696256
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	MAX	chr12:66695794-66696720	MCF-7	breast:	n/a	n/a
2	TAF1	chr12:66696187-66696628	GM12892	blood:	n/a	n/a
3	TBL1XR1	chr12:66696231-66696564	K562	blood:	n/a	n/a
4	MAFK	chr12:66695875-66696384	IMR90	lung:	n/a	n/a
5	MYC	chr12:66696121-66696507	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr12:66695827-66696762	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:66696173-66696666	K562	blood:	n/a	n/a
8	BCLAF1	chr12:66696153-66696769	GM12878	blood:	n/a	chr12:66696676-66696683 chr12:66696224-66696233 chr12:66696345-66696354
9	ARID3A	chr12:66696102-66696635	K562	blood:	n/a	n/a
10	ELF1	chr12:66695891-66696586	K562	blood:	n/a	chr12:66696280-66696289 chr12:66696279-66696290
11	EP300	chr12:66695837-66696653	K562	blood:	n/a	chr12:66696282-66696289 chr12:66696089-66696105
12	TAF1	chr12:66696160-66696625	K562	blood:	n/a	n/a
13	MXI1	chr12:66695889-66696711	Hela-S3	cervix:	n/a	n/a
14	GABPA	chr12:66696173-66696417	A549	lung:	n/a	n/a
15	POLR2A	chr12:66695969-66696744	Hela-S3	cervix:	n/a	n/a
16	TEAD4	chr12:66695892-66696616	K562	blood:	n/a	n/a
17	YY1	chr12:66696194-66696694	GM12892	blood:	n/a	n/a
18	CEBPB	chr12:66695919-66696459	Hela-S3	cervix:	n/a	chr12:66696313-66696321
19	STAT3	chr12:66696041-66696456	MCF10A-Er-Src	breast:	n/a	chr12:66696205-66696225 chr12:66696273-66696293 chr12:66696210-66696219 chr12:66696209-66696220 chr12:66696279-66696288 chr12:66696277-66696288 chr12:66696278-66696287 chr12:66696279-66696287 chr12:66696208-66696222 chr12:66696211-66696220
20	POU2F2	chr12:66696159-66696588	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:66696123-66696787	K562	blood:	n/a	n/a
22	MAX	chr12:66695940-66696722	K562	blood:	n/a	n/a
23	POLR2A	chr12:66696229-66696518	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr12:66695829-66696770	GM19099	blood:	n/a	n/a
25	BHLHE40	chr12:66695942-66696639	GM12878	blood:	n/a	n/a
26	RELA	chr12:66695762-66696609	GM19099	blood:	n/a	n/a
27	CTCF	chr12:66696140-66696290	GM12865	blood:	n/a	n/a
28	MAFF	chr12:66696203-66696470	K562	blood:	n/a	n/a
29	MXI1	chr12:66695107-66697212	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr12:66695815-66696630	HCT-116	colon:	n/a	n/a
31	GTF2F1	chr12:66695873-66696586	Hela-S3	cervix:	n/a	n/a
32	MAX	chr12:66695798-66696785	HepG2	liver:	n/a	n/a
33	ELF1	chr12:66696016-66696549	HepG2	liver:	n/a	chr12:66696280-66696289 chr12:66696279-66696290
34	STAT1	chr12:66695803-66696794	Hela-S3	cervix:	n/a	chr12:66696205-66696225 chr12:66696273-66696293 chr12:66696210-66696219 chr12:66696279-66696288 chr12:66696277-66696288 chr12:66696278-66696287 chr12:66696279-66696287 chr12:66696208-66696222 chr12:66696211-66696220
35	GABPA	chr12:66695806-66696618	MCF-7	breast:	n/a	n/a
36	MAZ	chr12:66695957-66696625	HepG2	liver:	n/a	n/a
37	POLR2A	chr12:66696133-66696575	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr12:66696155-66696551	K562	blood:	n/a	n/a
39	POLR2A	chr12:66696020-66696795	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr12:66696240-66696390	HBMEC	blood vessel:	n/a	n/a
41	GTF2B	chr12:66696095-66696529	K562	blood:	n/a	n/a
42	CTCF	chr12:66696255-66696293	Lung_OC	lung:	n/a	n/a
43	NFYB	chr12:66695993-66696556	K562	blood:	n/a	chr12:66696312-66696322 chr12:66696309-66696324 chr12:66696313-66696325 chr12:66696310-66696324 chr12:66696311-66696326 chr12:66696311-66696324 chr12:66696309-66696324
44	CREB1	chr12:66695949-66696533	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr12:66696218-66696588	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr12:66695698-66696886	MCF-7	breast:	n/a	n/a
47	CEBPD	chr12:66696170-66696420	HepG2	liver:	n/a	n/a
48	POLR2A	chr12:66696019-66696635	PANC-1	pancreas:	n/a	n/a
49	HMGN3	chr12:66695943-66696610	K562	blood:	n/a	n/a
50	ELF1	chr12:66696078-66696649	A549	lung:	n/a	chr12:66696280-66696289 chr12:66696279-66696290

No.	Distal block	Cell Line	Cell type
1	chr12:66695924..66696743-chr17:62222909..62223499,2	Hela-S3	cervix:
2	chr12:66523311..66525203-chr12:66696051..66697589,2	MCF-7	breast:
3	chr12:66696089..66696950-chr17:7486736..7487408,2	Hela-S3	cervix:
4	chr12:66563056..66564656-chr12:66694946..66697705,2	MCF-7	breast:
5	chr10:101380312..101381158-chr12:66695914..66696767,2	Hela-S3	cervix:

Variant related genes	Relation type
HELB	TF binding region
ENSG00000155957	Chromatin interaction
ENSG00000155287	Chromatin interaction
ENSG00000129255	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000260475	Chromatin interaction
ENSG00000233223	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000239335	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1009211	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10784523	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10784524	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10878401	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10878402	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs10878403	0.96[CEU][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11176125	0.96[CEU][hapmap];0.84[GIH][hapmap];0.96[EUR][1000 genomes]
rs11176126	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11176132	0.96[EUR][1000 genomes]
rs11610967	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs12146707	0.99[EUR][1000 genomes]
rs12146757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12146776	0.83[EUR][1000 genomes]
rs12822052	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1370125	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1495495	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1921013	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2028095	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2118138	1.00[CEU][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs2118139	1.00[CEU][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2118140	1.00[CEU][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs2904497	0.95[EUR][1000 genomes]
rs3741603	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3741604	0.89[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs4430553	1.00[CEU][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs6421217	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6581672	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6581676	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7131920	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7306114	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7308068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968129	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs974349	0.88[AMR][1000 genomes];0.95[EUR][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3741605	HELB	cis	cerebellum	SCAN
rs3741605	HELB	cis	parietal	SCAN
rs3741605	HELB	cis	Muscle Skeletal	GTEx
rs3741605	HELB	cis	multi-tissue	Pritchard
rs3741605	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs3741605	HELB	cis	Nerve Tibial	GTEx
rs3741605	HELB	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66694800-66698400	Active TSS	Rectal Smooth Muscle	rectum
2	chr12:66695200-66697200	Active TSS	Stomach Smooth Muscle	stomach
3	chr12:66695200-66698000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:66695400-66696400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:66695400-66696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:66695400-66696400	Active TSS	Adipose Nuclei	Adipose
7	chr12:66695400-66697000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:66695400-66697000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:66695400-66697000	Active TSS	Brain Hippocampus Middle	brain
10	chr12:66695400-66698400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr12:66695600-66696800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:66695600-66696800	Active TSS	Aorta	Aorta
13	chr12:66695600-66696800	Active TSS	Brain Angular Gyrus	brain
14	chr12:66695600-66696800	Active TSS	Brain Cingulate Gyrus	brain
15	chr12:66695600-66696800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:66695600-66696800	Active TSS	Fetal Heart	heart
17	chr12:66695600-66696800	Active TSS	Left Ventricle	heart
18	chr12:66695600-66696800	Active TSS	HSMMtube	muscle
19	chr12:66695600-66696800	Active TSS	NH-A	brain
20	chr12:66695600-66696800	Active TSS	NHDF-Ad	bronchial
21	chr12:66695600-66697000	Active TSS	Muscle Satellite Cultured Cells	--
22	chr12:66695600-66697000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:66695600-66697000	Active TSS	Brain Substantia Nigra	brain
24	chr12:66695600-66697000	Active TSS	Colon Smooth Muscle	Colon
25	chr12:66695600-66697000	Active TSS	Fetal Lung	lung
26	chr12:66695600-66697000	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:66695600-66697000	Active TSS	Fetal Muscle Leg	muscle
28	chr12:66695600-66697000	Active TSS	Ovary	ovary
29	chr12:66695600-66697000	Active TSS	Psoas Muscle	Psoas
30	chr12:66695600-66697000	Active TSS	Right Ventricle	heart
31	chr12:66695600-66697000	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr12:66695600-66697000	Active TSS	A549	lung
33	chr12:66695600-66697000	Active TSS	NHLF	lung
34	chr12:66695600-66697200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr12:66695600-66697200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:66695600-66697200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:66695600-66697200	Active TSS	Esophagus	oesophagus
38	chr12:66695600-66697200	Active TSS	Pancreas	Pancrea
39	chr12:66695600-66697400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:66695600-66697400	Active TSS	HMEC	breast
41	chr12:66695600-66697600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr12:66695600-66697600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:66695600-66697600	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr12:66695600-66697800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:66695600-66697800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:66695600-66697800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:66695600-66697800	Active TSS	Colonic Mucosa	Colon
48	chr12:66695800-66696400	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr12:66695800-66696800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr12:66695800-66696800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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