Variant report

Variant	rs6151653
Chromosome Location	chr5:79971612-79971613
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	chr5:79950445..79952547-chr5:79969128..79971891,2	MCF-7	breast:
2	chr5:79970108..79972408-chr5:79975282..79977185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113318	Chromatin interaction
ENSG00000228716	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs17205503	0.94[EUR][1000 genomes]
rs245392	0.96[CEU][hapmap];0.81[YRI][hapmap]
rs28059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs33008	0.92[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap]
rs6151604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861850	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6864493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6887400	0.85[ASN][1000 genomes]
rs73129108	0.87[AFR][1000 genomes]
rs73132417	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7712332	0.81[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6151653	SCAMP1	cis	parietal	SCAN
rs6151653	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs6151653	DHFR	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79951600-79972200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:79951600-80015600	Weak transcription	Small Intestine	intestine
3	chr5:79951800-79982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:79952200-79975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:79952400-79975400	Weak transcription	HSMMtube	muscle
6	chr5:79952400-79976600	Strong transcription	Fetal Thymus	thymus
7	chr5:79952400-79976800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr5:79952400-79983000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:79952600-79985200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:79952600-79991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:79952800-79972200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:79953200-79980800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:79956200-79979000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:79956400-80015600	Weak transcription	Psoas Muscle	Psoas
15	chr5:79958200-79998000	Weak transcription	Fetal Brain Male	brain
16	chr5:79961200-79977000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr5:79961600-79974000	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:79962800-80015600	Weak transcription	A549	lung
19	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
20	chr5:79963800-79979600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr5:79964000-79977800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:79964000-79984600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:79964000-79984800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:79964000-79998000	Weak transcription	Aorta	Aorta
25	chr5:79964200-79975000	Weak transcription	Fetal Brain Female	brain
26	chr5:79964400-79975400	Weak transcription	Colonic Mucosa	Colon
27	chr5:79964400-79977800	Weak transcription	Esophagus	oesophagus
28	chr5:79964400-79983200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:79964400-79999200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:79964600-79972800	Strong transcription	Primary B cells from cord blood	blood
31	chr5:79964600-79973000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:79964600-79974800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:79964600-79983000	Weak transcription	Brain Angular Gyrus	brain
34	chr5:79964800-79972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr5:79964800-79974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:79964800-79976800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr5:79964800-79998000	Weak transcription	Gastric	stomach
38	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:79965000-79975400	Weak transcription	Pancreas	Pancrea
40	chr5:79965000-79977200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr5:79965000-80021400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:79965200-79980400	Weak transcription	Brain Germinal Matrix	brain
43	chr5:79965600-79978400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:79965800-79973200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:79965800-79978400	Strong transcription	Dnd41	blood
46	chr5:79966000-79976200	Strong transcription	HSMM	muscle
47	chr5:79966000-79976600	Strong transcription	Fetal Intestine Large	intestine
48	chr5:79966200-79973200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:79967000-79977000	Strong transcription	Primary hematopoietic stem cells	blood
50	chr5:79968200-79971800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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