Variant report

Variant	rs7650998
Chromosome Location	chr3:46607255-46607256
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	chr3:46530235..46530934-chr3:46606775..46607619,4	K562	blood:
2	chr3:46526283..46528703-chr3:46605275..46607340,2	K562	blood:

Variant related genes	Relation type
ENSG00000012223	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1049667	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12185926	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13096172	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2001441	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3806702	0.81[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap]
rs3806703	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6783573	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs939408	0.89[AMR][1000 genomes];0.86[EUR][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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7650998	TDGF1	cis	lung	GTEx
rs7650998	TDGF1	cis	Esophagus Muscularis	GTEx
rs7650998	LRRC2	cis	cerebellum	SCAN
rs7650998	KIF15	cis	parietal	SCAN
rs7650998	MON1A	cis	parietal	SCAN
rs7650998	ATRIP	cis	parietal	SCAN
rs7650998	ALS2CL	cis	cerebellum	SCAN
rs7650998	TDGF1	cis	Adipose Subcutaneous	GTEx
rs7650998	CDCP1	cis	cerebellum	SCAN
rs7650998	TDGF1	cis	cerebellum	SCAN
rs7650998	TDGF1	cis	Muscle Skeletal	GTEx
rs7650998	TDGF1	cis	parietal	SCAN
rs7650998	TDGF1	cis	Nerve Tibial	GTEx
rs7650998	MAP4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46606200-46607600	Enhancers	Spleen	Spleen
2	chr3:46606200-46608000	Active TSS	Left Ventricle	heart
3	chr3:46606200-46608400	Active TSS	Right Ventricle	heart
4	chr3:46606400-46607400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr3:46606400-46608200	Active TSS	Psoas Muscle	Psoas
6	chr3:46606600-46607400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:46606600-46607600	Flanking Active TSS	HSMMtube	muscle
8	chr3:46606600-46607800	Bivalent Enhancer	Fetal Brain Male	brain
9	chr3:46606600-46608000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:46606600-46608000	Active TSS	Brain Angular Gyrus	brain
11	chr3:46606600-46608200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:46606800-46607400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:46606800-46607400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
14	chr3:46606800-46607400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
15	chr3:46606800-46607600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr3:46606800-46607800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:46606800-46608400	Active TSS	Ovary	ovary
18	chr3:46607000-46607400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:46607000-46607400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:46607000-46607400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:46607000-46607400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:46607000-46607400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:46607000-46607400	Bivalent Enhancer	K562	blood
24	chr3:46607000-46607600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr3:46607000-46607600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:46607000-46607600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:46607000-46607600	Flanking Active TSS	Liver	Liver
28	chr3:46607000-46607600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr3:46607000-46607600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr3:46607000-46607600	Flanking Active TSS	Thymus	Thymus
31	chr3:46607000-46607600	Flanking Active TSS	HSMM	muscle
32	chr3:46607000-46607800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:46607000-46607800	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr3:46607000-46607800	Flanking Active TSS	NH-A	brain
35	chr3:46607000-46608000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:46607000-46608000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:46607000-46608000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:46607000-46608000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
39	chr3:46607000-46608000	Bivalent/Poised TSS	Fetal Kidney	kidney
40	chr3:46607000-46608000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
41	chr3:46607000-46608000	Active TSS	Osteobl	bone
42	chr3:46607000-46608200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:46607000-46608200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:46607000-46608200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr3:46607000-46608200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:46607000-46608200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:46607000-46608200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:46607000-46608200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:46607000-46608200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:46607000-46608200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle

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