Variant report

Variant	rs2899077
Chromosome Location	chr15:43510025-43510026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43509970-43511857	PBDE	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:43509980-43510030	Hepatocyte	liver:	n/a
2	chr15:43509980-43510030	HCF	heart:	n/a
3	chr15:43509980-43510030	IMR90	lung:	fetal
4	chr15:43509980-43510030	RPTEC	kidney:	n/a
5	chr15:43509980-43510030	HUVEC	blood vessel:	n/a
6	chr15:43509980-43510030	Hela-S3	cervix:	n/a
7	chr15:43509980-43510030	HMEC	breast:	n/a
8	chr15:43509980-43510030	SK-N-MC	brain:	n/a
9	chr15:43509980-43510030	AG10803	skin:	n/a
10	chr15:43509980-43510030	MCF10A-Er-Src	breast:	n/a
11	chr15:43509980-43510030	BJ	skin:	n/a
12	chr15:43509980-43510030	GM12891	blood:	n/a
13	chr15:43509980-43510030	BE2_C	brain:	n/a
14	chr15:43509980-43510030	H1-hESC	embryonic stem cell:	embryo
15	chr15:43509980-43510030	HPAEpiC	pulmonary alveolar:	n/a
16	chr15:43509980-43510030	HCPEpiC	choroid plexus:	n/a
17	chr15:43509980-43510030	NHBE	bronchial:	n/a
18	chr15:43509980-43510030	NH-A	brain:	n/a
19	chr15:43509980-43510030	HCT-116	colon:	n/a
20	chr15:43509980-43510030	SAEC	small airway:	n/a
21	chr15:43509980-43510030	K562	blood:	n/a
22	chr15:43509980-43510030	HEK293	kidney:	embryo
23	chr15:43509980-43510030	ProgFib	skin:	n/a
24	chr15:43509980-43510030	PrEC	prostate:	n/a
25	chr15:43509980-43510030	SK-N-SH_RA	brain:	n/a
26	chr15:43509980-43510030	AoSMC	blood vessel:	n/a
27	chr15:43509980-43510030	HEEpiC	esophagus:	n/a
28	chr15:43509980-43510030	HNPCEpiC	eye:	n/a
29	chr15:43509980-43510030	GM12892	blood:	n/a
30	chr15:43509980-43510030	HepG2	liver:	n/a
31	chr15:43509980-43510030	U87	brain:	n/a
32	chr15:43509980-43510030	HCM	heart:	n/a
33	chr15:43509980-43510030	HRE	kidney:	n/a
34	chr15:43509980-43510030	HRCEpiC	kidney:	n/a
35	chr15:43509980-43510030	SK-N-SH	brain:	n/a
36	chr15:43509980-43510030	MCF-7	breast:	n/a
37	chr15:43509980-43510030	HAEpiC	amniotic membrane:	n/a
38	chr15:43509980-43510030	NHDF-neo	bronchial:	n/a
39	chr15:43509980-43510030	ovcar-3	ovarian:	n/a
40	chr15:43509980-43510030	PANC-1	pancreas:	n/a
41	chr15:43509980-43510030	SKMC	muscle:	n/a
42	chr15:43509980-43510030	GM19239	blood:	n/a
43	chr15:43509980-43510030	LNCaP	prostate:	n/a
44	chr15:43509980-43510030	HIPEpiC	eye:	n/a
45	chr15:43509980-43510030	PFSK-1	brain:	n/a
46	chr15:43509980-43510030	GM06990	blood:	n/a
47	chr15:43509980-43510030	Jurkat	blood:	n/a
48	chr15:43509980-43510030	ECC-1	luminal epithelium:	n/a
49	chr15:43509980-43510030	T-47D	breast:	n/a
50	chr15:43509980-43510030	HRPEpiC	eye:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43478750..43480959-chr15:43508624..43510280,2	K562	blood:
2	chr15:43500895..43503914-chr15:43509088..43512078,3	K562	blood:

No data

Variant related genes	Relation type
EPB42	TF binding region
EPB42	CpG island
ENSG00000166947	Chromatin interaction
ENSG00000166946	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11070386	0.89[CEU][hapmap];0.94[CHB][hapmap]
rs11070391	0.89[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs11070396	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11070397	0.87[EUR][1000 genomes]
rs11070398	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630595	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs11855754	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12592725	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899266	0.89[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs1462856	0.89[CEU][hapmap];0.81[MEX][hapmap]
rs16957511	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1834643	0.91[EUR][1000 genomes]
rs2042742	0.92[EUR][1000 genomes]
rs2241516	1.00[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412752	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs28585036	0.86[CEU][hapmap]
rs28756768	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2947019	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs34646108	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784267	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3784268	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4573908	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4924704	0.89[CEU][hapmap];0.81[MEX][hapmap]
rs494863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495286	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs497138	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs499280	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs530305	1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531850	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs538218	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs540587	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493076	0.89[CEU][hapmap];0.81[MEX][hapmap]
rs6493077	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap]
rs7174915	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7183814	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027371	0.86[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap]
rs8027733	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2899077	CCNDBP1	cis	Lymphoblastoid	GTEx
rs2899077	CCNDBP1	cis	lymphoblastoid	seeQTL
rs2899077	CCNDBP1	cis	multi-tissue	Pritchard
rs2899077	TGM5	cis	lymphoblastoid	seeQTL
rs2899077	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43489800-43513200	Weak transcription	Right Atrium	heart
2	chr15:43501600-43511000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:43504200-43510800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:43506400-43518600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:43508200-43510600	Weak transcription	NHEK	skin
6	chr15:43509000-43511200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:43510000-43511600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:43510000-43512400	Enhancers	K562	blood

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