Variant report

Variant	rs7640470
Chromosome Location	chr3:100210509-100210510
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	MXI1	chr3:100210419-100212102	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:100210418-100212116	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100203629..100205546-chr3:100208727..100210663,2	MCF-7	breast:

Variant related genes	Relation type
TMEM45A	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11920006	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11926280	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12631075	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12634371	0.93[ASN][1000 genomes]
rs4132537	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4928098	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57018910	0.94[ASN][1000 genomes]
rs58059387	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59771628	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61636409	0.95[ASN][1000 genomes]
rs62276517	0.84[ASN][1000 genomes]
rs62276527	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6441285	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6789867	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7429072	0.94[ASN][1000 genomes]
rs7429604	0.94[ASN][1000 genomes]
rs7616839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7619507	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7630198	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7640470	COL8A1	cis	cerebellum	SCAN
rs7640470	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs7640470	TMEM45A	cis	multi-tissue	Pritchard
rs7640470	TMEM45A	cis	lymphoblastoid	seeQTL
rs7640470	IMPG2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100205000-100210800	Weak transcription	K562	blood
2	chr3:100206600-100210600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:100209600-100210600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:100209600-100210800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:100210000-100210600	Enhancers	Fetal Brain Female	brain
6	chr3:100210000-100210600	Enhancers	HMEC	breast
7	chr3:100210000-100210800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:100210200-100210600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:100210200-100210600	Enhancers	Fetal Heart	heart
10	chr3:100210200-100210600	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr3:100210200-100210800	Weak transcription	Psoas Muscle	Psoas
12	chr3:100210400-100210600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:100210400-100210600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:100210400-100210600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr3:100210400-100210600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:100210400-100210600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:100210400-100210600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:100210400-100210600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr3:100210400-100210600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:100210400-100210600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:100210400-100210600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:100210400-100210600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:100210400-100210600	Enhancers	Adipose Nuclei	Adipose
24	chr3:100210400-100210600	Enhancers	Brain Angular Gyrus	brain
25	chr3:100210400-100210600	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr3:100210400-100210600	Enhancers	Fetal Muscle Leg	muscle
27	chr3:100210400-100210600	Enhancers	GM12878-XiMat	blood
28	chr3:100210400-100210600	Enhancers	Hela-S3	cervix
29	chr3:100210400-100210600	Enhancers	HSMMtube	muscle
30	chr3:100210400-100210600	Enhancers	NHDF-Ad	bronchial
31	chr3:100210400-100210600	Enhancers	NHEK	skin
32	chr3:100210400-100210600	Enhancers	Osteobl	bone
33	chr3:100210400-100210800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:100210400-100210800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:100210400-100210800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:100210400-100210800	Flanking Active TSS	NHLF	lung
37	chr3:100210400-100211000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:100210400-100211000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:100210400-100211000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:100210400-100211000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:100210400-100211000	Flanking Active TSS	Liver	Liver
42	chr3:100210400-100211000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
43	chr3:100210400-100211000	Flanking Active TSS	Fetal Lung	lung
44	chr3:100210400-100211000	Flanking Active TSS	Fetal Stomach	stomach
45	chr3:100210400-100212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:100210400-100212200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:100210400-100212600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:100210400-100212600	Active TSS	Brain Anterior Caudate	brain

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