Variant report

Variant	rs6873068
Chromosome Location	chr5:108089189-108089190
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:108087050..108092037-chr5:108092288..108095333,5	K562	blood:
2	chr5:108083882..108086165-chr5:108087597..108089755,2	K562	blood:
3	chr5:108073242..108074795-chr5:108088832..108091578,2	K562	blood:
4	chr5:108063411..108065243-chr5:108088881..108091712,2	MCF-7	breast:
5	chr5:108082550..108087144-chr5:108087711..108092491,6	MCF-7	breast:
6	chr5:108062389..108066599-chr5:108086966..108090381,3	MCF-7	breast:
7	chr5:108088004..108090580-chr5:108268352..108270013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272523	Chromatin interaction
ENSG00000151422	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10044305	0.90[AFR][1000 genomes]
rs10060694	0.89[AFR][1000 genomes]
rs1022045	0.94[ASN][1000 genomes]
rs10477431	0.89[AFR][1000 genomes]
rs1109617	0.96[ASN][1000 genomes]
rs11240982	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11739006	0.93[ASN][1000 genomes]
rs12153703	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13173714	0.96[ASN][1000 genomes]
rs1423457	0.96[ASN][1000 genomes]
rs17161476	0.94[ASN][1000 genomes]
rs2081126	0.90[AFR][1000 genomes]
rs2081129	0.88[AFR][1000 genomes]
rs2900035	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34660781	0.90[ASN][1000 genomes]
rs35398495	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4957789	0.93[ASN][1000 genomes]
rs6594333	0.93[ASN][1000 genomes]
rs6594334	0.96[ASN][1000 genomes]
rs6594336	0.94[ASN][1000 genomes]
rs6594338	0.89[AFR][1000 genomes]
rs6871143	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6871239	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6882107	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6889550	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6889967	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6891194	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6892439	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7700630	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7712956	0.84[AFR][1000 genomes]
rs7716320	0.94[ASN][1000 genomes]
rs7716485	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7716498	0.94[ASN][1000 genomes]
rs7726708	0.88[AFR][1000 genomes]
rs9285863	0.96[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6873068	FER	cis	Artery Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108085600-108091000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:108085600-108102600	Weak transcription	Lung	lung
3	chr5:108085600-108119800	Weak transcription	Left Ventricle	heart
4	chr5:108085800-108089200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:108085800-108089400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:108085800-108089400	Weak transcription	HSMM	muscle
7	chr5:108085800-108089400	Weak transcription	HSMMtube	muscle
8	chr5:108085800-108094400	Weak transcription	Brain Anterior Caudate	brain
9	chr5:108085800-108095200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:108085800-108095200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:108085800-108095400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:108085800-108095400	Weak transcription	A549	lung
13	chr5:108085800-108097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:108085800-108097800	Weak transcription	Brain Angular Gyrus	brain
15	chr5:108086200-108092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:108086200-108095400	Weak transcription	Primary T cells from cord blood	blood
17	chr5:108086200-108095400	Weak transcription	Fetal Lung	lung
18	chr5:108086200-108095600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:108086200-108119200	Weak transcription	Fetal Kidney	kidney
20	chr5:108086200-108120600	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:108086400-108089400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:108086400-108094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:108086400-108095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:108086600-108091000	Weak transcription	Fetal Brain Male	brain
25	chr5:108086800-108089400	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:108087000-108089400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:108087600-108089400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr5:108087600-108089800	Enhancers	Hela-S3	cervix
29	chr5:108087600-108090200	Enhancers	Osteobl	bone
30	chr5:108088000-108089400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:108088200-108089400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:108088200-108089600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr5:108088200-108090000	Enhancers	Adipose Nuclei	Adipose
34	chr5:108088400-108089400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:108088400-108089600	Active TSS	GM12878-XiMat	blood
36	chr5:108088400-108095400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:108088600-108089400	Active TSS	HMEC	breast
38	chr5:108088600-108097800	Weak transcription	Gastric	stomach
39	chr5:108088800-108089200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:108088800-108089200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:108088800-108089200	Active TSS	NHLF	lung
42	chr5:108088800-108089400	Active TSS	NHEK	skin
43	chr5:108089000-108089200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:108089000-108089200	Enhancers	NH-A	brain
45	chr5:108089000-108089400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:108089000-108089400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:108089000-108090200	Enhancers	NHDF-Ad	bronchial

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