Variant report

Variant	rs7604067
Chromosome Location	chr2:55653269-55653270
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55646192..55651046-chr2:55651862..55657167,5	K562	blood:
2	chr2:55652771..55655244-chr2:55659480..55661281,2	K562	blood:
3	chr2:55652880..55655236-chr2:55657266..55660173,3	MCF-7	breast:
4	chr2:55651546..55653549-chr2:55657687..55659327,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10169061	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10187983	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191937	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125573	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11886931	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11902837	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617887	0.81[AMR][1000 genomes]
rs12621495	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12623605	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713293	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713294	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713295	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713296	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713298	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991401	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13001912	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13010237	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13010255	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13013113	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13022424	0.81[AMR][1000 genomes]
rs13389156	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13423775	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349884	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1349885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1902060	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2198575	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2867174	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2867175	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2867176	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28672687	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36052911	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828235	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56978967	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66882175	0.84[EUR][1000 genomes]
rs6746104	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6747649	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6752182	0.84[EUR][1000 genomes]
rs6756777	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74181227	0.84[EUR][1000 genomes]
rs7572492	0.83[EUR][1000 genomes]
rs7589390	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7606505	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7604067	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:55650000-55653400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:55650000-55659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:55651000-55653400	Enhancers	HMEC	breast
6	chr2:55651200-55653400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:55651200-55653400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:55651600-55653400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:55651600-55653400	Enhancers	NHEK	skin
10	chr2:55652000-55653400	Enhancers	NHLF	lung
11	chr2:55652200-55653400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:55652200-55653400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:55652200-55653400	Flanking Active TSS	Hela-S3	cervix
14	chr2:55652200-55653400	Enhancers	NH-A	brain
15	chr2:55652400-55653400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:55652400-55653400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55652400-55653400	Enhancers	Stomach Mucosa	stomach
18	chr2:55652400-55653400	Flanking Active TSS	A549	lung
19	chr2:55652400-55653400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:55652800-55653400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:55652800-55653400	Enhancers	Spleen	Spleen
22	chr2:55653200-55657000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:55653200-55657400	Weak transcription	HUVEC	blood vessel
24	chr2:55653200-55657400	Weak transcription	Osteobl	bone
25	chr2:55653200-55657600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:55653200-55658000	Weak transcription	NHDF-Ad	bronchial

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