Variant report

Variant	rs820869
Chromosome Location	chr5:73980065-73980066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr5:73979992-73980191	HepG2	liver:	n/a	chr5:73980098-73980109 chr5:73980093-73980114
2	GTF2F1	chr5:73980057-73980098	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr5:73979887-73980176	H1-hESC	embryonic stem cell:	n/a	chr5:73980098-73980109 chr5:73980093-73980114

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:73980039-73980089	SK-N-MC	brain:	n/a
2	chr5:73980039-73980089	NHDF-neo	bronchial:	n/a
3	chr5:73980039-73980089	HPAEpiC	pulmonary alveolar:	n/a
4	chr5:73980039-73980089	HCF	heart:	n/a
5	chr5:73980039-73980089	HUVEC	blood vessel:	n/a
6	chr5:73980039-73980089	RPTEC	kidney:	n/a
7	chr5:73980039-73980089	AG09309	skin:	n/a
8	chr5:73980039-73980089	HCM	heart:	n/a
9	chr5:73980039-73980089	GM12891	blood:	n/a
10	chr5:73980039-73980089	ovcar-3	ovarian:	n/a
11	chr5:73980039-73980089	NT2-D1	testis:	n/a
12	chr5:73980039-73980089	Caco-2	colon:	n/a
13	chr5:73980039-73980089	SK-N-SH_RA	brain:	n/a
14	chr5:73980039-73980089	U87	brain:	n/a
15	chr5:73980039-73980089	NB4	blood:	n/a
16	chr5:73980039-73980089	H1-hESC	embryonic stem cell:	embryo
17	chr5:73980039-73980089	AoSMC	blood vessel:	n/a
18	chr5:73980039-73980089	ECC-1	luminal epithelium:	n/a
19	chr5:73980039-73980089	GM19239	blood:	n/a
20	chr5:73980039-73980089	HL-60	blood:	n/a
21	chr5:73980039-73980089	CMK	blood:	n/a
22	chr5:73980039-73980089	SKMC	muscle:	n/a
23	chr5:73980039-73980089	NHBE	bronchial:	n/a
24	chr5:73980039-73980089	AG04450	lung:	fetal
25	chr5:73980039-73980089	HIPEpiC	eye:	n/a
26	chr5:73980039-73980089	HNPCEpiC	eye:	n/a
27	chr5:73980039-73980089	HRPEpiC	eye:	n/a
28	chr5:73980039-73980089	Hepatocyte	liver:	n/a
29	chr5:73980039-73980089	PFSK-1	brain:	n/a
30	chr5:73980039-73980089	HEEpiC	esophagus:	n/a
31	chr5:73980039-73980089	K562	blood:	n/a
32	chr5:73980039-73980089	NH-A	brain:	n/a
33	chr5:73980039-73980089	GM12892	blood:	n/a
34	chr5:73980039-73980089	LNCaP	prostate:	n/a
35	chr5:73980039-73980089	ProgFib	skin:	n/a
36	chr5:73980039-73980089	SAEC	small airway:	n/a
37	chr5:73980039-73980089	MCF10A-Er-Src	breast:	n/a
38	chr5:73980039-73980089	Hela-S3	cervix:	n/a
39	chr5:73980039-73980089	A549	lung:	n/a
40	chr5:73980039-73980089	HMEC	breast:	n/a
41	chr5:73980039-73980089	AG10803	skin:	n/a
42	chr5:73980039-73980089	HAEpiC	amniotic membrane:	n/a
43	chr5:73980039-73980089	HCPEpiC	choroid plexus:	n/a
44	chr5:73980039-73980089	BE2_C	brain:	n/a
45	chr5:73980039-73980089	Jurkat	blood:	n/a
46	chr5:73980039-73980089	AG04449	skin:	fetal
47	chr5:73980039-73980089	HepG2	liver:	n/a
48	chr5:73980039-73980089	SK-N-SH	brain:	n/a
49	chr5:73980039-73980089	GM12878	blood:	n/a
50	chr5:73980039-73980089	HCT-116	colon:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr5:73979598..73982392-chr5:73983812..73990818,9	MCF-7	breast:
2	chr5:73979909..73982593-chr5:73987219..73990536,5	MCF-7	breast:
3	chr5:72857771..72859719-chr5:73979974..73981658,2	K562	blood:
4	chr5:73980002..73981869-chr5:74633426..74635131,2	K562	blood:
5	chr5:73978938..73982006-chr5:74061565..74064417,3	K562	blood:
6	chr5:73979743..73983565-chr5:73984545..73990071,12	K562	blood:
7	chr5:73979647..73982006-chr5:74061742..74064417,2	K562	blood:

No data

Variant related genes	Relation type
HEXB	TF binding region
HEXB	CpG island
ENSG00000164346	Chromatin interaction
ENSG00000113161	Chromatin interaction
ENSG00000049860	Chromatin interaction
ENSG00000164347	Chromatin interaction
ENSG00000164331	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2936918	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3104693	0.80[EUR][1000 genomes]
rs6896615	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs820841	0.85[EUR][1000 genomes]
rs820862	0.85[EUR][1000 genomes]
rs820863	0.85[EUR][1000 genomes]
rs820866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820867	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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]
rs820871	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs820872	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs820874	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs820876	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs820879	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs820880	0.94[ASW][hapmap];0.87[LWK][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs820881	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs820882	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs820883	0.94[ASW][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs820885	0.94[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs820887	0.82[AFR][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	esv13844	chr5:73979961-73993853	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs820869	TMEM174	cis	parietal	SCAN
rs820869	HEXB	cis	cerebellum	SCAN
rs820869	MAP1B	cis	parietal	SCAN
rs820869	HEXB	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73966800-73980200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:73966800-73980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:73969800-73980600	Weak transcription	HMEC	breast
4	chr5:73969800-73980600	Weak transcription	HSMM	muscle
5	chr5:73969800-73980800	Weak transcription	NHLF	lung
6	chr5:73971800-73980200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:73973800-73980600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:73975200-73980200	Weak transcription	Spleen	Spleen
9	chr5:73976000-73980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:73976200-73980200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:73976200-73980600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:73976200-73980600	Weak transcription	Osteobl	bone
13	chr5:73976200-73981000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:73976400-73980200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:73976400-73980200	Weak transcription	Hela-S3	cervix
16	chr5:73976800-73980600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:73977400-73980800	Weak transcription	HSMMtube	muscle
18	chr5:73978400-73980600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:73978400-73980600	Enhancers	Fetal Intestine Large	intestine
20	chr5:73978600-73980600	Enhancers	Fetal Intestine Small	intestine
21	chr5:73979000-73980200	Weak transcription	A549	lung
22	chr5:73979000-73980800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:73979000-73980800	Weak transcription	NH-A	brain
24	chr5:73979200-73980600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:73979200-73980600	Weak transcription	NHEK	skin
26	chr5:73979200-73980800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:73979400-73980600	Enhancers	Placenta	Placenta
28	chr5:73980000-73980400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:73980000-73980400	Bivalent Enhancer	HepG2	liver
30	chr5:73980000-73980400	Enhancers	K562	blood
31	chr5:73980000-73980600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr5:73980000-73981600	Active TSS	iPS-20b Cell Line	embryonic stem cell

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