Variant report

Variant	rs1451807
Chromosome Location	chr5:118965219-118965220
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:118965199-118965249	HAEpiC	amniotic membrane:	n/a
2	chr5:118965199-118965249	Hepatocyte	liver:	n/a
3	chr5:118965199-118965249	H1-hESC	embryonic stem cell:	embryo
4	chr5:118965199-118965249	GM12892	blood:	n/a
5	chr5:118965199-118965249	Jurkat	blood:	n/a
6	chr5:118965199-118965249	IMR90	lung:	fetal
7	chr5:118965199-118965249	MCF-7	breast:	n/a
8	chr5:118965202-118965252	GM12892	blood:	n/a
9	chr5:118965202-118965252	ovcar-3	ovarian:	n/a
10	chr5:118965202-118965252	HNPCEpiC	eye:	n/a
11	chr5:118965199-118965249	T-47D	breast:	n/a
12	chr5:118965199-118965249	SK-N-SH_RA	brain:	n/a
13	chr5:118965202-118965252	IMR90	lung:	fetal
14	chr5:118965199-118965249	HCT-116	colon:	n/a
15	chr5:118965199-118965249	BJ	skin:	n/a
16	chr5:118965199-118965249	SKMC	muscle:	n/a
17	chr5:118965202-118965252	HRCEpiC	kidney:	n/a
18	chr5:118965199-118965249	Caco-2	colon:	n/a
19	chr5:118965202-118965252	SAEC	small airway:	n/a
20	chr5:118965199-118965249	HUVEC	blood vessel:	n/a
21	chr5:118965202-118965252	HMEC	breast:	n/a
22	chr5:118965202-118965252	H1-hESC	embryonic stem cell:	embryo
23	chr5:118965199-118965249	RPTEC	kidney:	n/a
24	chr5:118965199-118965249	SK-N-SH	brain:	n/a
25	chr5:118965199-118965249	AG09309	skin:	n/a
26	chr5:118965202-118965252	Caco-2	colon:	n/a
27	chr5:118965199-118965249	HCM	heart:	n/a
28	chr5:118965202-118965252	Jurkat	blood:	n/a
29	chr5:118965199-118965249	PANC-1	pancreas:	n/a
30	chr5:118965202-118965252	HPAEpiC	pulmonary alveolar:	n/a
31	chr5:118965202-118965252	U87	brain:	n/a
32	chr5:118965202-118965252	SK-N-MC	brain:	n/a
33	chr5:118965202-118965252	MCF-7	breast:	n/a
34	chr5:118965202-118965252	NHBE	bronchial:	n/a
35	chr5:118965199-118965249	ECC-1	luminal epithelium:	n/a
36	chr5:118965202-118965252	PFSK-1	brain:	n/a
37	chr5:118965202-118965252	Hela-S3	cervix:	n/a
38	chr5:118965202-118965252	HAEpiC	amniotic membrane:	n/a
39	chr5:118965199-118965249	HRE	kidney:	n/a
40	chr5:118965199-118965249	ProgFib	skin:	n/a
41	chr5:118965202-118965252	MCF10A-Er-Src	breast:	n/a
42	chr5:118965202-118965252	BE2_C	brain:	n/a
43	chr5:118965199-118965249	CMK	blood:	n/a
44	chr5:118965199-118965249	NB4	blood:	n/a
45	chr5:118965202-118965252	ECC-1	luminal epithelium:	n/a
46	chr5:118965202-118965252	T-47D	breast:	n/a
47	chr5:118965199-118965249	HEEpiC	esophagus:	n/a
48	chr5:118965199-118965249	MCF10A-Er-Src	breast:	n/a
49	chr5:118965202-118965252	CMK	blood:	n/a
50	chr5:118965199-118965249	HCPEpiC	choroid plexus:	n/a

No data

Variant related genes	Relation type
FAM170A	CpG island

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1318067	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs170609	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2243773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434599	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434601	0.90[EUR][1000 genomes]
rs2561512	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2561518	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2600410	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs328666	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs328695	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs328696	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs328697	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs328699	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs328705	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721674	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882777	chr5:118870452-118981480	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1451807	SNX24	cis	parietal	SCAN
rs1451807	HSD17B4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118964200-118969200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:118964400-118966600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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