Variant report

Variant	rs3741604
Chromosome Location	chr12:66696410-66696411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000129255	Chromatin interaction
ENSG00000155287	Chromatin interaction
ENSG00000260475	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000239335	Chromatin interaction
ENSG00000139233	Chromatin interaction
ENSG00000233223	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1009211	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784520	0.85[CHB][hapmap]
rs10784523	0.98[EUR][1000 genomes]
rs10878401	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878402	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878403	0.92[CEU][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs11176125	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11176126	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11176132	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176137	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11176142	0.89[CHB][hapmap]
rs11610967	0.90[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12146707	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12146757	0.99[EUR][1000 genomes]
rs12146776	0.84[EUR][1000 genomes]
rs12423377	0.84[CHB][hapmap]
rs12822052	0.96[EUR][1000 genomes]
rs1370125	0.95[EUR][1000 genomes]
rs1921013	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028095	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118138	0.89[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2118139	0.89[CEU][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs2118140	0.88[CEU][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2870780	0.84[CHB][hapmap]
rs2904497	0.95[EUR][1000 genomes]
rs3741605	0.89[CEU][hapmap];0.91[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs4430553	0.89[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs6421217	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6581672	0.95[EUR][1000 genomes]
rs7131920	0.98[EUR][1000 genomes]
rs7306114	0.95[EUR][1000 genomes]
rs7308068	0.91[CEU][hapmap];0.99[EUR][1000 genomes]
rs7968129	0.94[EUR][1000 genomes]
rs974349	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3741604	HELB	cis	cerebellum	SCAN
rs3741604	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs3741604	HELB	cis	Muscle Skeletal	GTEx
rs3741604	HELB	cis	parietal	SCAN
rs3741604	HELB	cis	Nerve Tibial	GTEx

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	chr12:66695400-66697000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:66695400-66697000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:66695400-66697000	Active TSS	Brain Hippocampus Middle	brain
7	chr12:66695400-66698400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:66695600-66696800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:66695600-66696800	Active TSS	Aorta	Aorta
10	chr12:66695600-66696800	Active TSS	Brain Angular Gyrus	brain
11	chr12:66695600-66696800	Active TSS	Brain Cingulate Gyrus	brain
12	chr12:66695600-66696800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:66695600-66696800	Active TSS	Fetal Heart	heart
14	chr12:66695600-66696800	Active TSS	Left Ventricle	heart
15	chr12:66695600-66696800	Active TSS	HSMMtube	muscle
16	chr12:66695600-66696800	Active TSS	NH-A	brain
17	chr12:66695600-66696800	Active TSS	NHDF-Ad	bronchial
18	chr12:66695600-66697000	Active TSS	Muscle Satellite Cultured Cells	--
19	chr12:66695600-66697000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:66695600-66697000	Active TSS	Brain Substantia Nigra	brain
21	chr12:66695600-66697000	Active TSS	Colon Smooth Muscle	Colon
22	chr12:66695600-66697000	Active TSS	Fetal Lung	lung
23	chr12:66695600-66697000	Active TSS	Fetal Muscle Trunk	muscle
24	chr12:66695600-66697000	Active TSS	Fetal Muscle Leg	muscle
25	chr12:66695600-66697000	Active TSS	Ovary	ovary
26	chr12:66695600-66697000	Active TSS	Psoas Muscle	Psoas
27	chr12:66695600-66697000	Active TSS	Right Ventricle	heart
28	chr12:66695600-66697000	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr12:66695600-66697000	Active TSS	A549	lung
30	chr12:66695600-66697000	Active TSS	NHLF	lung
31	chr12:66695600-66697200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr12:66695600-66697200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:66695600-66697200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:66695600-66697200	Active TSS	Esophagus	oesophagus
35	chr12:66695600-66697200	Active TSS	Pancreas	Pancrea
36	chr12:66695600-66697400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:66695600-66697400	Active TSS	HMEC	breast
38	chr12:66695600-66697600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr12:66695600-66697600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:66695600-66697600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr12:66695600-66697800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:66695600-66697800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr12:66695600-66697800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:66695600-66697800	Active TSS	Colonic Mucosa	Colon
45	chr12:66695800-66696800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:66695800-66696800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:66695800-66696800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:66695800-66696800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:66695800-66696800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
50	chr12:66695800-66696800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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