Variant report

Variant	rs60028471
Chromosome Location	chr3:100061251-100061252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100058351..100061697-chr3:100061751..100064533,3	MCF-7	breast:
2	chr3:100055058..100056849-chr3:100060980..100063043,2	MCF-7	breast:
3	chr3:100056621..100059013-chr3:100060542..100063010,3	K562	blood:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

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]
rs11720172	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927693	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17279967	0.85[EUR][1000 genomes]
rs2289501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272643	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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: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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60028471	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs60028471	TOMM70A	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	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
7	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:100054800-100061400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:100054800-100062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:100054800-100062800	Weak transcription	HUVEC	blood vessel
11	chr3:100054800-100064200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:100054800-100064600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:100054800-100064600	Weak transcription	NHLF	lung
14	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
15	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
16	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
17	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
18	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
21	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:100055000-100062800	Weak transcription	Hela-S3	cervix
23	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:100055200-100062600	Weak transcription	K562	blood
27	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:100055200-100071000	Weak transcription	HepG2	liver
29	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:100057000-100069600	Strong transcription	Dnd41	blood
31	chr3:100057200-100061800	Strong transcription	Osteobl	bone
32	chr3:100057200-100066800	Strong transcription	HSMM	muscle
33	chr3:100057200-100069200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:100057200-100069600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:100057400-100069600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:100057600-100061400	Strong transcription	Brain Hippocampus Middle	brain
37	chr3:100057600-100066200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:100057600-100069200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:100057600-100069600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:100057600-100069600	Strong transcription	Adipose Nuclei	Adipose
41	chr3:100057800-100061600	Strong transcription	Fetal Intestine Large	intestine
42	chr3:100057800-100062000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:100057800-100066200	Strong transcription	HMEC	breast
44	chr3:100057800-100069600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:100057800-100071400	Weak transcription	Fetal Heart	heart
46	chr3:100058000-100061600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:100058000-100061600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:100058000-100063400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:100058000-100065800	Strong transcription	A549	lung
50	chr3:100058000-100069600	Strong transcription	Primary monocytes fromperipheralblood	blood

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