Variant report

Variant	rs7619507
Chromosome Location	chr3:100211602-100211603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:1618873..1619547-chr3:100210982..100211748,2	Hela-S3	cervix:
2	chr22:38301815..38302566-chr3:100211020..100211628,2	Hela-S3	cervix:
3	chr12:48147196..48147737-chr3:100210846..100211663,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000100139	Chromatin interaction
ENSG00000186594	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11920006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11923942	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11926280	0.88[ASN][1000 genomes]
rs11927516	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12636805	0.94[ASN][1000 genomes]
rs12639465	0.81[JPT][hapmap]
rs4132537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4928097	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4928098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58059387	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59299896	0.95[ASN][1000 genomes]
rs59771628	0.97[ASN][1000 genomes]
rs60071944	0.95[ASN][1000 genomes]
rs62276520	0.95[ASN][1000 genomes]
rs62276521	0.95[ASN][1000 genomes]
rs62276522	0.92[ASN][1000 genomes]
rs62276523	0.92[ASN][1000 genomes]
rs62276526	0.88[ASN][1000 genomes]
rs62276527	0.88[ASN][1000 genomes]
rs6441285	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6441300	0.82[JPT][hapmap]
rs6763079	0.94[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs6763178	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67774605	0.95[ASN][1000 genomes]
rs6789867	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73152126	0.90[ASN][1000 genomes]
rs7430698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7430715	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7616839	1.00[CEU][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7630198	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7640470	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]
rs7653196	0.82[JPT][hapmap]
rs9813069	0.80[ASN][1000 genomes]
rs9851429	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][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
rs7619507	IMPG2	cis	cerebellum	SCAN
rs7619507	TMEM45A	cis	multi-tissue	Pritchard
rs7619507	COL8A1	cis	cerebellum	SCAN
rs7619507	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs7619507	TMEM45A	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100210400-100212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:100210400-100212200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:100210400-100212600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:100210400-100212600	Active TSS	Brain Anterior Caudate	brain
5	chr3:100210600-100211800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:100210600-100211800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:100210600-100212000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:100210600-100212000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:100210600-100212000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:100210600-100212000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:100210600-100212000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:100210600-100212000	Active TSS	Brain Substantia Nigra	brain
13	chr3:100210600-100212000	Active TSS	Fetal Heart	heart
14	chr3:100210600-100212000	Active TSS	Pancreas	Pancrea
15	chr3:100210600-100212000	Active TSS	Right Ventricle	heart
16	chr3:100210600-100212200	Active TSS	Brain Germinal Matrix	brain
17	chr3:100210600-100212200	Active TSS	Brain Hippocampus Middle	brain
18	chr3:100210600-100212200	Active TSS	Fetal Muscle Trunk	muscle
19	chr3:100210600-100212200	Active TSS	A549	lung
20	chr3:100210600-100212400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:100210600-100212400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:100210600-100212400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:100210600-100212400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:100210600-100212400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:100210600-100212400	Active TSS	Rectal Smooth Muscle	rectum
26	chr3:100210600-100212400	Active TSS	Right Atrium	heart
27	chr3:100210600-100212400	Active TSS	Stomach Smooth Muscle	stomach
28	chr3:100210600-100212800	Active TSS	HSMM	muscle
29	chr3:100210800-100211800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:100210800-100211800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:100210800-100211800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:100210800-100211800	Active TSS	Left Ventricle	heart
33	chr3:100210800-100211800	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr3:100210800-100211800	Active TSS	Stomach Mucosa	stomach
35	chr3:100210800-100212000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr3:100210800-100212000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr3:100210800-100212000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:100210800-100212000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:100210800-100212000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:100210800-100212000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
41	chr3:100210800-100212000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:100210800-100212000	Active TSS	Colon Smooth Muscle	Colon
43	chr3:100210800-100212000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:100210800-100212000	Active TSS	Fetal Thymus	thymus
45	chr3:100210800-100212000	Active TSS	Psoas Muscle	Psoas
46	chr3:100210800-100212000	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr3:100210800-100212000	Bivalent/Poised TSS	Thymus	Thymus
48	chr3:100210800-100212200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:100210800-100212200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr3:100210800-100212200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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