Variant report

Variant	rs11902837
Chromosome Location	chr2:55650940-55650941
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55644949..55647772-chr2:55649501..55651559,3	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10169061	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10169395	0.80[ASN][1000 genomes]
rs10172058	0.81[AMR][1000 genomes]
rs10187983	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191937	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10496042	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11125564	0.80[AMR][1000 genomes]
rs11125571	0.83[ASN][1000 genomes]
rs11125573	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11678347	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11886931	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12614357	0.84[AMR][1000 genomes]
rs12617887	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12621289	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12621495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623605	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713293	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713294	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713295	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12713296	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713298	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991401	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13001912	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13010237	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13010255	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13013113	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13019339	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13022424	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13028925	0.80[AMR][1000 genomes]
rs13389156	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13423775	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1349885	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1370360	0.84[AMR][1000 genomes]
rs1902060	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2198575	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2867174	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2867175	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2867176	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2867177	0.82[AMR][1000 genomes]
rs28672687	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36052911	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791652	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3828235	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56978967	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66882175	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6746104	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752182	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6754930	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6756777	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74181227	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7561473	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7569535	0.82[AMR][1000 genomes]
rs7572492	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7589390	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7600339	0.83[AMR][1000 genomes]
rs7604067	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7606505	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789365	0.83[AMR][1000 genomes];0.82[EUR][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
rs11902837	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55648000-55651000	Weak transcription	HMEC	breast
3	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:55648000-55651600	Weak transcription	NHEK	skin
5	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel
7	chr2:55648000-55652200	Weak transcription	NH-A	brain
8	chr2:55648000-55652400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:55648000-55652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55648000-55652400	Weak transcription	HSMM	muscle
11	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:55648200-55651000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:55648200-55651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:55648200-55652200	Weak transcription	Osteobl	bone
16	chr2:55648400-55651800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:55648400-55652400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:55648400-55652400	Enhancers	A549	lung
19	chr2:55648400-55652400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:55648600-55651000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:55648600-55651200	Weak transcription	K562	blood
22	chr2:55649200-55651000	Weak transcription	NHLF	lung
23	chr2:55649400-55651400	Weak transcription	NHDF-Ad	bronchial
24	chr2:55649400-55652200	Enhancers	Hela-S3	cervix
25	chr2:55649600-55651200	Enhancers	Brain Hippocampus Middle	brain
26	chr2:55649600-55653000	Enhancers	HepG2	liver
27	chr2:55650000-55651200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:55650000-55652400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:55650000-55653400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:55650000-55659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55650200-55651000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:55650200-55652400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:55650400-55652400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:55650600-55651800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:55650800-55651800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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