Variant report

Variant	rs729228
Chromosome Location	chr8:48573973-48573974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:48570759..48574488-chr8:48583570..48586841,4	K562	blood:
2	chr8:48573288..48575298-chr8:48647992..48650663,2	MCF-7	breast:
3	chr8:48571104..48575817-chr8:48648052..48653139,6	K562	blood:
4	chr8:48573853..48575397-chr8:48576919..48578598,2	MCF-7	breast:
5	chr8:48572699..48576050-chr8:48649206..48652243,4	MCF-7	breast:
6	chr8:48572127..48574593-chr8:48609264..48610909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164808	Chromatin interaction
ENSG00000221869	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10088698	0.83[TSI][hapmap]
rs10092880	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10095193	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10107723	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10958274	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1487438	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16927869	1.00[ASW][hapmap]
rs28542855	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3614	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4873477	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs58297550	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6992255	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7002441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs72646358	0.83[EUR][1000 genomes]
rs72646361	0.87[EUR][1000 genomes]
rs72646363	0.81[EUR][1000 genomes]
rs72646372	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72646383	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7812323	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7822320	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7830743	0.80[EUR][1000 genomes]
rs7838910	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7841661	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7843066	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8178238	1.00[CEU][hapmap]
rs9918758	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs729228	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48565600-48574400	Weak transcription	Aorta	Aorta
2	chr8:48570400-48575000	Enhancers	Pancreas	Pancrea
3	chr8:48571200-48574800	Enhancers	Brain Angular Gyrus	brain
4	chr8:48571200-48574800	Enhancers	Psoas Muscle	Psoas
5	chr8:48571600-48574800	Enhancers	Colonic Mucosa	Colon
6	chr8:48571600-48574800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr8:48571600-48576200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr8:48571600-48577000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:48572200-48574400	Flanking Active TSS	Fetal Heart	heart
10	chr8:48572200-48574800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:48572200-48574800	Enhancers	Ovary	ovary
12	chr8:48572200-48575000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:48572400-48575000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr8:48572600-48574200	Enhancers	Brain Cingulate Gyrus	brain
15	chr8:48572600-48574200	Enhancers	Fetal Intestine Large	intestine
16	chr8:48572600-48574400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr8:48572600-48574400	Enhancers	Stomach Mucosa	stomach
18	chr8:48572600-48574600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr8:48572600-48574800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:48572600-48574800	Enhancers	Brain Anterior Caudate	brain
21	chr8:48572600-48574800	Enhancers	Left Ventricle	heart
22	chr8:48572600-48574800	Enhancers	HSMM	muscle
23	chr8:48572600-48575000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr8:48572600-48575800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:48572600-48577000	Enhancers	Placenta	Placenta
26	chr8:48572800-48574000	Flanking Active TSS	Liver	Liver
27	chr8:48572800-48574400	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr8:48572800-48574800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr8:48572800-48574800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:48572800-48574800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr8:48572800-48574800	Enhancers	Fetal Stomach	stomach
32	chr8:48572800-48575000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr8:48572800-48575000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr8:48572800-48575000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr8:48572800-48575800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr8:48572800-48575800	Weak transcription	Fetal Brain Female	brain
37	chr8:48572800-48576400	Enhancers	Fetal Muscle Leg	muscle
38	chr8:48572800-48578400	Weak transcription	Primary B cells from cord blood	blood
39	chr8:48573000-48574400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr8:48573000-48574800	Enhancers	Right Atrium	heart
41	chr8:48573000-48574800	Enhancers	Small Intestine	intestine
42	chr8:48573000-48575000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr8:48573000-48576000	Enhancers	Esophagus	oesophagus
44	chr8:48573000-48577000	Enhancers	Lung	lung
45	chr8:48573000-48582600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr8:48573200-48574000	Enhancers	HepG2	liver
47	chr8:48573200-48574600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr8:48573200-48574600	Enhancers	Brain Hippocampus Middle	brain
49	chr8:48573200-48574600	Enhancers	Fetal Lung	lung
50	chr8:48573200-48574800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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