Variant report

Variant	rs2099188
Chromosome Location	chr2:56069151-56069152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:56004031..56006518-chr2:56068498..56070427,2	MCF-7	breast:
2	chr2:56068913..56070987-chr2:56145608..56147872,2	MCF-7	breast:
3	chr2:56036866..56038749-chr2:56067694..56069314,2	MCF-7	breast:
4	chr2:56066504..56070179-chr2:56070783..56074906,3	MCF-7	breast:
5	chr2:56067724..56069716-chr2:56075621..56077306,2	MCF-7	breast:
6	chr2:55843068..55844575-chr2:56068438..56069941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10173540	0.90[ASN][1000 genomes]
rs10180043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196888	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12104451	0.94[ASN][1000 genomes]
rs13394642	0.92[ASN][1000 genomes]
rs13409792	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13413609	0.80[ASN][1000 genomes]
rs13426650	0.96[ASN][1000 genomes]
rs28744383	0.92[ASN][1000 genomes]
rs4519567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58754091	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723695	0.90[ASN][1000 genomes]
rs72807739	0.96[ASN][1000 genomes]
rs72807740	0.96[ASN][1000 genomes]
rs7577580	0.90[ASN][1000 genomes]
rs7604558	0.92[ASN][1000 genomes]
rs875997	0.87[AFR][1000 genomes];0.94[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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2099188	C2orf63	cis	parietal	SCAN
rs2099188	RPL23AP32	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56064200-56069400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:56064800-56070200	Weak transcription	K562	blood
3	chr2:56066600-56069600	Weak transcription	Small Intestine	intestine
4	chr2:56066800-56069200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56066800-56069600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:56066800-56069800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:56066800-56070600	Weak transcription	Liver	Liver
8	chr2:56066800-56082600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:56067400-56069200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:56067400-56069200	Weak transcription	HSMM	muscle
11	chr2:56067600-56070000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:56067600-56070000	Weak transcription	HSMMtube	muscle
13	chr2:56067600-56070200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:56067800-56069200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:56067800-56070200	Weak transcription	HMEC	breast
16	chr2:56068000-56069200	Weak transcription	NHEK	skin
17	chr2:56068400-56069600	Enhancers	Pancreas	Pancrea
18	chr2:56068400-56070200	Enhancers	Hela-S3	cervix
19	chr2:56068600-56070000	Enhancers	Stomach Mucosa	stomach
20	chr2:56068600-56071400	Flanking Active TSS	A549	lung
21	chr2:56068600-56071800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:56068800-56069200	Enhancers	Gastric	stomach
23	chr2:56068800-56070400	Enhancers	Placenta	Placenta
24	chr2:56068800-56071000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:56068800-56071200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:56068800-56071400	Enhancers	Fetal Intestine Small	intestine
27	chr2:56068800-56072000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:56068800-56072000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:56068800-56072000	Enhancers	Osteobl	bone
30	chr2:56069000-56069400	Enhancers	Adipose Nuclei	Adipose
31	chr2:56069000-56071000	Enhancers	HepG2	liver
32	chr2:56069000-56071200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr2:56069000-56071400	Enhancers	Fetal Intestine Large	intestine
34	chr2:56069000-56071600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:56069000-56071600	Enhancers	NHDF-Ad	bronchial
36	chr2:56069000-56071600	Enhancers	NHLF	lung
37	chr2:56069000-56072200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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