Variant report

Variant	rs7560480
Chromosome Location	chr2:114518482-114518483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:114517696-114518566	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr2:114517784-114518534	SK-N-SH	brain:	n/a	n/a
3	EP300	chr2:114517851-114518580	SK-N-SH	brain:	n/a	n/a
4	MEF2A	chr2:114517910-114518603	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr2:114517802-114518558	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr2:114517797-114518582	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr2:114517864-114518553	SK-N-SH	brain:	n/a	n/a
8	USF1	chr2:114518123-114518523	SK-N-SH	brain:	n/a	n/a
9	JUND	chr2:114517831-114518490	SK-N-SH	brain:	n/a	chr2:114518350-114518359
10	MEF2A	chr2:114517866-114518525	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:114517804-114518578	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:114512582..114515674-chr2:114516372..114520568,3	MCF-7	breast:
2	chr2:114516554..114518950-chr2:114645999..114648586,2	K562	blood:
3	chr2:114496162..114498041-chr2:114518174..114520618,2	K562	blood:
4	chr2:114512297..114513973-chr2:114517803..114519961,2	MCF-7	breast:
5	chr2:114514378..114516716-chr2:114517485..114519813,3	MCF-7	breast:
6	chr2:114511479..114519908-chr2:114641728..114650266,13	MCF-7	breast:
7	chr2:114514479..114516685-chr2:114517501..114519701,2	K562	blood:

No data

Variant related genes	Relation type
SLC35F5	TF binding region
ENSG00000115091	Chromatin interaction
ENSG00000115084	Chromatin interaction
ENSG00000270019	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10167730	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10172842	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10177576	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179657	0.92[EUR][1000 genomes]
rs10209098	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12711788	0.81[EUR][1000 genomes]
rs1375332	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2122097	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2290108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305255	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2442136	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2687627	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28451366	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2900744	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36062527	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3816384	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3890789	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848343	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4848345	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4849270	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4849277	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4849279	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6711542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7577893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7600228	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv2883	chr2:114507889-114535199	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7560480	RPL23AP7	cis	Muscle Skeletal	GTEx
rs7560480	RPL23AP7	cis	Whole Blood	GTEx
rs7560480	SLC35F5	Cis_1M	lymphoblastoid	RTeQTL
rs7560480	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs7560480	RPL23AP7	cis	lung	GTEx
rs7560480	RPL23AP7	cis	Artery Tibial	GTEx
rs7560480	DDX11L2	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114515200-114519000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:114515200-114519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:114515200-114519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:114515200-114520400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:114515200-114520400	Weak transcription	Left Ventricle	heart
6	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:114515400-114519000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:114515400-114519600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:114515400-114519800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:114515400-114519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:114515400-114519800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:114515400-114519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:114515400-114520000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:114515600-114519800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:114515600-114521600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:114517400-114521000	Enhancers	NHDF-Ad	bronchial
17	chr2:114517600-114519200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:114517600-114520200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:114517600-114520200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:114517600-114520400	Enhancers	HSMMtube	muscle
21	chr2:114517600-114521200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:114517800-114518800	Enhancers	NH-A	brain
23	chr2:114517800-114519800	Enhancers	Osteobl	bone
24	chr2:114517800-114520800	Enhancers	HSMM	muscle
25	chr2:114517800-114520800	Enhancers	HUVEC	blood vessel
26	chr2:114517800-114520800	Enhancers	NHLF	lung
27	chr2:114517800-114521200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:114518000-114519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:114518000-114520800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:114518200-114519200	Enhancers	Psoas Muscle	Psoas
31	chr2:114518200-114519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:114518400-114519200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:114518400-114519800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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