Variant report

Variant	rs9873033
Chromosome Location	chr3:100072332-100072333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100042421..100044566-chr3:100070698..100073226,2	K562	blood:
2	chr3:100066721..100069295-chr3:100070418..100073671,4	MCF-7	breast:
3	chr3:100067925..100070797-chr3:100070813..100073426,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10511179	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919543	0.80[ASN][1000 genomes]
rs11919627	0.81[ASN][1000 genomes]
rs16842142	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs17279967	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3772687	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs55864663	0.83[ASN][1000 genomes]
rs56012915	0.83[ASN][1000 genomes]
rs57332305	0.83[ASN][1000 genomes]
rs57703319	0.83[ASN][1000 genomes]
rs59304656	0.81[ASN][1000 genomes]
rs59396265	0.81[ASN][1000 genomes]
rs59491720	0.83[ASN][1000 genomes]
rs59507591	0.81[ASN][1000 genomes]
rs59509062	0.81[ASN][1000 genomes]
rs60463428	0.83[ASN][1000 genomes]
rs60999188	0.83[ASN][1000 genomes]
rs72941452	0.83[ASN][1000 genomes]
rs72941453	0.83[ASN][1000 genomes]
rs72941454	0.83[ASN][1000 genomes]
rs72941473	0.83[ASN][1000 genomes]
rs72941482	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9873033	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs9873033	NIT2	cis	multi-tissue	Pritchard
rs9873033	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
5	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:100069400-100082400	Weak transcription	Fetal Brain Male	brain
8	chr3:100069600-100080600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:100069600-100083800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:100069600-100085800	Weak transcription	Small Intestine	intestine
11	chr3:100069600-100087000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:100070800-100072600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:100071000-100072400	Genic enhancers	HepG2	liver
14	chr3:100071000-100072600	Genic enhancers	Fetal Intestine Large	intestine
15	chr3:100071000-100072800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:100071000-100072800	Strong transcription	Osteobl	bone
17	chr3:100071000-100073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:100071000-100073200	Genic enhancers	Liver	Liver
19	chr3:100071000-100074000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr3:100071000-100074600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:100071000-100074800	Strong transcription	Fetal Brain Female	brain
22	chr3:100071000-100075000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:100071000-100075000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr3:100071000-100075200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:100071000-100075200	Strong transcription	Fetal Thymus	thymus
26	chr3:100071000-100075400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:100071000-100075400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:100071000-100075400	Strong transcription	Primary B cells from cord blood	blood
29	chr3:100071000-100075400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:100071000-100075400	Strong transcription	Placenta	Placenta
31	chr3:100071000-100075600	Strong transcription	Primary T cells from cord blood	blood
32	chr3:100071000-100075800	Strong transcription	GM12878-XiMat	blood
33	chr3:100071000-100076400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr3:100071000-100076400	Strong transcription	HSMM	muscle
35	chr3:100071000-100077600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:100071000-100080800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:100071000-100087800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:100071000-100087800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:100071000-100093600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:100071200-100072400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:100071200-100072400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr3:100071200-100072400	Strong transcription	NH-A	brain
45	chr3:100071200-100072600	Strong transcription	Hela-S3	cervix
46	chr3:100071200-100072800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:100071200-100073200	Strong transcription	Esophagus	oesophagus
48	chr3:100071200-100073200	Strong transcription	Fetal Lung	lung
49	chr3:100071200-100073200	Strong transcription	NHLF	lung
50	chr3:100071200-100073400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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