Variant report

Variant	rs3790608
Chromosome Location	chr1:113055023-113055024
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	RFX5	chr1:113054036-113055164	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113053649..113055695-chr1:113241407..113243136,2	K562	blood:
2	chr1:113053258..113055489-chr1:113072240..113074967,2	MCF-7	breast:
3	chr1:112937399..112939003-chr1:113054969..113056954,2	MCF-7	breast:

Variant related genes	Relation type
WNT2B	TF binding region
ENSG00000143079	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3748655	1.00[CEU][hapmap]
rs3790598	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs3790609	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
rs3790608	WNT2B	cis	parietal	SCAN
rs3790608	ST7L	cis	lymphoblastoid	seeQTL
rs3790608	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs3790608	UBE1L	trans	lymphoblastoid	RTeQTL
rs3790608	ST7L	cis	multi-tissue	Pritchard
rs3790608	GSTM2	cis	parietal	SCAN
rs3790608	GSTM1	cis	parietal	SCAN
rs3790608	AMPD1	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr1:113052600-113055200	Weak transcription	Lung	lung
13	chr1:113052600-113057600	Weak transcription	Gastric	stomach
14	chr1:113053000-113059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:113053200-113055600	Enhancers	Ovary	ovary
16	chr1:113054000-113055400	Enhancers	Fetal Stomach	stomach
17	chr1:113054200-113056400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:113054400-113055400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:113054600-113055800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:113054600-113056000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:113054600-113066800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:113054800-113055600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:113055000-113055200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr1:113055000-113055200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:113055000-113055200	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:113055000-113055200	Enhancers	Small Intestine	intestine
27	chr1:113055000-113055400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr1:113055000-113056000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:113055000-113056000	Enhancers	HUVEC	blood vessel
30	chr1:113055000-113056600	Enhancers	Placenta	Placenta
31	chr1:113055000-113057000	Enhancers	Esophagus	oesophagus
32	chr1:113055000-113058000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:113055000-113058800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:113055000-113059000	Enhancers	NHLF	lung
35	chr1:113055000-113059400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:113055000-113067000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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