Variant report

Variant	rs3790609
Chromosome Location	chr1:113056990-113056991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113050916..113052536-chr1:113056260..113057826,2	K562	blood:

Variant related genes	Relation type
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12138754	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3737136	0.81[TSI][hapmap]
rs3790598	0.89[GIH][hapmap];1.00[TSI][hapmap]
rs3790608	0.90[TSI][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1008375	chr1:113028271-113060221	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1009068	chr1:113048992-113057407	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3790609	PHTF1	cis	parietal	SCAN
rs3790609	GSTM2	cis	parietal	SCAN
rs3790609	ST7L	cis	lymphoblastoid	seeQTL
rs3790609	AMPD1	cis	cerebellum	SCAN
rs3790609	GSTM1	cis	parietal	SCAN
rs3790609	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs3790609	SYT6	cis	parietal	SCAN
rs3790609	WNT2B	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113051800-113059800	Weak transcription	Aorta	Aorta
2	chr1:113052000-113059600	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:113052200-113057600	Weak transcription	Right Atrium	heart
5	chr1:113052200-113057600	Weak transcription	Right Ventricle	heart
6	chr1:113052200-113058200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:113052200-113059600	Weak transcription	Pancreas	Pancrea
8	chr1:113052200-113067600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:113052400-113059400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:113052400-113067000	Weak transcription	Adipose Nuclei	Adipose
12	chr1:113052600-113057600	Weak transcription	Gastric	stomach
13	chr1:113053000-113059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:113054600-113066800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:113055000-113057000	Enhancers	Esophagus	oesophagus
16	chr1:113055000-113058000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:113055000-113058800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:113055000-113059000	Enhancers	NHLF	lung
19	chr1:113055000-113059400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:113055000-113067000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:113055200-113057000	Enhancers	Colonic Mucosa	Colon
22	chr1:113055200-113058200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:113055200-113059400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:113055400-113057600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:113055600-113057600	Weak transcription	Ovary	ovary
26	chr1:113055600-113059000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:113055800-113058000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:113055800-113059600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:113055800-113067200	Weak transcription	Fetal Lung	lung
30	chr1:113055800-113067600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
32	chr1:113056000-113057600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:113056000-113058200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:113056000-113058800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:113056000-113059200	Weak transcription	NHEK	skin
36	chr1:113056000-113059400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:113056000-113067600	Weak transcription	HUVEC	blood vessel
38	chr1:113056200-113057200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:113056400-113057400	Enhancers	Fetal Stomach	stomach
40	chr1:113056400-113057800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:113056400-113057800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:113056400-113059000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:113056400-113059800	Weak transcription	Lung	lung
44	chr1:113056600-113057400	Weak transcription	Osteobl	bone
45	chr1:113056600-113058000	Weak transcription	HSMM	muscle
46	chr1:113056600-113058400	Enhancers	K562	blood
47	chr1:113056600-113066800	Weak transcription	Placenta	Placenta
48	chr1:113056800-113057000	Enhancers	HSMMtube	muscle
49	chr1:113056800-113057800	Weak transcription	Stomach Mucosa	stomach

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