Variant report

Variant	rs2289501
Chromosome Location	chr3:100058300-100058301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
2	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1036768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045610	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10511179	0.81[CEU][hapmap]
rs10936193	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs11720172	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927693	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17279967	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2068018	0.80[CEU][hapmap]
rs41272643	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60028471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150325	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73150329	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73150348	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73150350	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3387925	chr3:100056362-100059860	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2289501	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL
rs2289501	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
8	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
12	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
14	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:100054800-100058400	Weak transcription	NH-A	brain
16	chr3:100054800-100058600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:100054800-100058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:100054800-100058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:100054800-100058800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:100054800-100059400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:100054800-100059400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:100054800-100060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:100054800-100060000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:100054800-100060200	Weak transcription	Right Ventricle	heart
25	chr3:100054800-100060600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:100054800-100061400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:100054800-100062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:100054800-100062800	Weak transcription	HUVEC	blood vessel
29	chr3:100054800-100064200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:100054800-100064600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:100054800-100064600	Weak transcription	NHLF	lung
32	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
33	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
34	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
35	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
36	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
39	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:100055000-100058400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:100055000-100058400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:100055000-100058400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:100055000-100059600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:100055000-100059800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:100055000-100059800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:100055000-100060200	Weak transcription	Fetal Kidney	kidney
47	chr3:100055000-100060600	Weak transcription	GM12878-XiMat	blood
48	chr3:100055000-100062800	Weak transcription	Hela-S3	cervix
49	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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