Variant report

Variant	rs6998258
Chromosome Location	chr8:67039389-67039390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:67038868..67041219-chr8:67343383..67346327,3	MCF-7	breast:
2	chr8:67024747..67027371-chr8:67038783..67042182,4	MCF-7	breast:
3	chr8:67035768..67039915-chr8:67339207..67342855,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246145	Chromatin interaction
ENSG00000147576	Chromatin interaction
ENSG00000253190	Chromatin interaction
ENSG00000179041	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10096789	0.87[EUR][1000 genomes]
rs10098823	1.00[CEU][hapmap]
rs10099957	0.83[GIH][hapmap]
rs10104916	0.83[GIH][hapmap]
rs10109602	0.83[GIH][hapmap]
rs11779150	1.00[CEU][hapmap]
rs12156080	1.00[CEU][hapmap]
rs13439818	0.83[EUR][1000 genomes]
rs16932564	0.83[GIH][hapmap]
rs3176921	0.83[GIH][hapmap]
rs34083382	0.84[EUR][1000 genomes]
rs55640054	0.92[EUR][1000 genomes]
rs55691225	0.87[EUR][1000 genomes]
rs55745275	0.87[EUR][1000 genomes]
rs56163324	0.92[EUR][1000 genomes]
rs56176008	0.90[EUR][1000 genomes]
rs57390453	0.92[EUR][1000 genomes]
rs61738600	0.92[EUR][1000 genomes]
rs6472244	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs6472245	0.83[GIH][hapmap]
rs6472250	0.84[YRI][hapmap]
rs6982394	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs6983227	0.92[EUR][1000 genomes]
rs6986947	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs6990486	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs6992031	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6992434	0.92[EUR][1000 genomes]
rs6998761	0.83[GIH][hapmap]
rs6999780	0.83[GIH][hapmap]
rs7005882	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7006209	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs7006394	0.83[GIH][hapmap]
rs7006903	0.83[GIH][hapmap]
rs7008138	0.82[YRI][hapmap]
rs7010547	0.92[EUR][1000 genomes]
rs7013524	0.83[GIH][hapmap]
rs73236728	0.82[EUR][1000 genomes]
rs749328	0.87[EUR][1000 genomes]
rs7813194	0.87[EUR][1000 genomes]
rs7813201	0.87[EUR][1000 genomes]
rs7820617	0.83[GIH][hapmap]
rs7822243	0.83[GIH][hapmap]
rs7831234	0.83[GIH][hapmap]
rs7838582	0.92[EUR][1000 genomes]
rs7839635	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7842761	0.83[GIH][hapmap]
rs7843038	0.83[GIH][hapmap]
rs7843436	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7845017	0.92[EUR][1000 genomes]
rs884325	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs959302	0.87[EUR][1000 genomes]
rs9694082	0.83[GIH][hapmap]

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	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3414665	chr8:66936816-67381935	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6998258	TRIM55	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:67036800-67039400	Weak transcription	Psoas Muscle	Psoas
2	chr8:67036800-67044800	Weak transcription	Pancreas	Pancrea
3	chr8:67036800-67044800	Weak transcription	Spleen	Spleen
4	chr8:67036800-67046400	Enhancers	NHLF	lung
5	chr8:67036800-67047000	Enhancers	NHDF-Ad	bronchial
6	chr8:67036800-67047200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:67037000-67040200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:67037200-67040200	Weak transcription	Adipose Nuclei	Adipose
9	chr8:67037200-67040600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:67037200-67042200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr8:67037400-67040200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:67037400-67040600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr8:67037400-67042400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr8:67037600-67040200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:67037600-67040200	Weak transcription	Osteobl	bone
16	chr8:67037600-67041800	Weak transcription	Hela-S3	cervix
17	chr8:67037800-67039600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:67037800-67040200	Weak transcription	NH-A	brain
19	chr8:67037800-67040800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:67037800-67041800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:67038000-67040400	Weak transcription	NHEK	skin
22	chr8:67038000-67040600	Weak transcription	HMEC	breast
23	chr8:67038400-67040200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:67038600-67039400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:67038800-67039400	Flanking Active TSS	Liver	Liver
26	chr8:67038800-67039400	Enhancers	GM12878-XiMat	blood
27	chr8:67038800-67039400	Flanking Active TSS	HSMMtube	muscle
28	chr8:67038800-67039600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr8:67038800-67039600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr8:67038800-67040400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:67038800-67040400	Active TSS	Fetal Heart	heart
32	chr8:67038800-67040400	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr8:67038800-67040800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr8:67038800-67042600	Active TSS	Fetal Muscle Trunk	muscle
35	chr8:67038800-67042600	Active TSS	Right Atrium	heart
36	chr8:67038800-67043800	Active TSS	Right Ventricle	heart
37	chr8:67039000-67039400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr8:67039000-67039400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:67039000-67039400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:67039000-67039400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr8:67039000-67039400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr8:67039000-67039400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr8:67039000-67039400	Active TSS	Fetal Kidney	kidney
44	chr8:67039000-67039400	Enhancers	Fetal Muscle Leg	muscle
45	chr8:67039000-67039400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr8:67039000-67039400	Enhancers	K562	blood
47	chr8:67039000-67039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr8:67039000-67039600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr8:67039000-67039600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr8:67039000-67039600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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