Variant report

Variant	rs13255477
Chromosome Location	chr8:99057903-99057904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:435)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:435 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr8:99057549-99058166	GM12878	blood:	n/a	n/a
2	UBTF	chr8:99057588-99058755	K562	blood:	n/a	n/a
3	MAX	chr8:99057068-99058062	GM12878	blood:	n/a	n/a
4	POLR2A	chr8:99055687-99058203	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr8:99057408-99058145	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr8:99056948-99057937	A549	lung:	n/a	n/a
7	GABPA	chr8:99057172-99058812	MCF-7	breast:	n/a	chr8:99057829-99057836
8	SIN3AK20	chr8:99057255-99058228	PANC-1	pancreas:	n/a	n/a
9	MAX	chr8:99057309-99058249	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr8:99057661-99058166	A549	lung:	n/a	n/a
11	SMARCB1	chr8:99056927-99058699	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr8:99056335-99058089	GM12891	blood:	n/a	n/a
13	ELF1	chr8:99057437-99058084	HepG2	liver:	n/a	n/a
14	FOS	chr8:99057741-99057987	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr8:99057344-99058137	MCF10A-Er-Src	breast:	n/a	n/a
16	SIN3A	chr8:99057181-99058643	GM12878	blood:	n/a	chr8:99058533-99058541 chr8:99058502-99058511
17	NFYB	chr8:99057739-99058036	K562	blood:	n/a	n/a
18	TAF1	chr8:99057382-99058646	H1-hESC	embryonic stem cell:	n/a	n/a
19	GABPA	chr8:99057640-99058002	HepG2	liver:	n/a	chr8:99057829-99057836
20	SIN3AK20	chr8:99057209-99058194	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr8:99057520-99058506	GM12878	blood:	n/a	n/a
22	TAF1	chr8:99057245-99058242	PFSK-1	brain:	n/a	n/a
23	TAF7	chr8:99057285-99058266	H1-hESC	embryonic stem cell:	n/a	n/a
24	PBX3	chr8:99057572-99058020	A549	lung:	n/a	n/a
25	POLR2A	chr8:99056290-99058759	HCT-116	colon:	n/a	n/a
26	PML	chr8:99057408-99058213	K562	blood:	n/a	n/a
27	CEBPB	chr8:99057663-99058023	Hela-S3	cervix:	n/a	n/a
28	GABPA	chr8:99057439-99058212	GM12878	blood:	n/a	chr8:99057829-99057836
29	POLR2A	chr8:99056370-99058124	K562	blood:	n/a	n/a
30	YY1	chr8:99057238-99058395	A549	lung:	n/a	chr8:99057750-99057760 chr8:99057748-99057760 chr8:99057751-99057759 chr8:99057742-99057762
31	POLR2A	chr8:99056253-99058172	HL-60	blood:	n/a	n/a
32	RELA	chr8:99057418-99058123	GM10847	blood:	n/a	n/a
33	MXI1	chr8:99057130-99058598	Hela-S3	cervix:	n/a	n/a
34	MYC	chr8:99057069-99058769	NB4	blood:	n/a	n/a
35	TAF1	chr8:99057259-99058289	ECC-1	luminal epithelium:	n/a	n/a
36	GABPA	chr8:99057641-99057996	GM12878	blood:	n/a	chr8:99057829-99057836
37	POLR2A	chr8:99057092-99058363	ProgFib	skin:	n/a	n/a
38	YY1	chr8:99057400-99058440	HCT-116	colon:	n/a	chr8:99057750-99057760 chr8:99058404-99058418 chr8:99057748-99057760 chr8:99057751-99057759 chr8:99057742-99057762
39	SIN3AK20	chr8:99057475-99058026	PANC-1	pancreas:	n/a	n/a
40	SP1	chr8:99057358-99058252	A549	lung:	n/a	chr8:99057854-99057863 chr8:99057852-99057864
41	POLR2A	chr8:99057631-99058010	HepG2	liver:	n/a	n/a
42	RAD21	chr8:99057538-99058611	IMR90	lung:	n/a	chr8:99058571-99058581
43	MXI1	chr8:99057029-99058734	HepG2	liver:	n/a	n/a
44	POLR2A	chr8:99056293-99058153	GM12892	blood:	n/a	n/a
45	REST	chr8:99057465-99058166	PFSK-1	brain:	n/a	chr8:99057692-99057705
46	TCF12	chr8:99057385-99058245	ECC-1	luminal epithelium:	n/a	chr8:99057872-99057882
47	JUND	chr8:99057845-99058024	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF1	chr8:99057544-99058019	Hela-S3	cervix:	n/a	n/a
49	BHLHE40	chr8:99057405-99058035	GM12878	blood:	n/a	n/a
50	POLR2A	chr8:99054646-99059519	SK-N-MC	brain:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:99039510..99041898-chr8:99055972..99058591,2	K562	blood:
2	chr2:113403023..113403716-chr8:99057580..99058281,2	HCT-116	colon:
3	chr8:99054883..99058427-chr8:99128521..99131598,4	K562	blood:
4	chr8:98799001..98802379-chr8:99056110..99059171,3	K562	blood:
5	chr16:4420182..4421961-chr8:99056269..99057971,2	MCF-7	breast:
6	chr8:99054385..99060040-chr8:99125093..99131908,20	MCF-7	breast:
7	chr11:62609117..62609635-chr8:99057523..99058278,2	NB4	blood:
8	chr8:98880240..98884584-chr8:99054888..99058750,6	MCF-7	breast:
9	chr8:99055858..99058755-chr8:99126907..99132454,7	K562	blood:
10	chr1:149816826..149819259-chr8:99056422..99059164,2	MCF-7	breast:
11	chr8:99055062..99058733-chr8:99305548..99307498,3	MCF-7	breast:
12	chr8:98787186..98788825-chr8:99057177..99058975,2	MCF-7	breast:
13	chr8:98656009..98658499-chr8:99057409..99059369,2	MCF-7	breast:
14	chr8:98787259..98790021-chr8:99056219..99059277,4	MCF-7	breast:
15	chr8:99054555..99060747-chr8:99127722..99132697,23	MCF-7	breast:
16	chr7:105750764..105753718-chr8:99056330..99059303,2	MCF-7	breast:
17	chr8:87524372..87527585-chr8:99056393..99058902,3	MCF-7	breast:
18	chr17:57914601..57916569-chr8:99057138..99058947,2	MCF-7	breast:
19	chr8:99056304..99059597-chr8:99060333..99064411,5	K562	blood:
20	chr8:99054937..99059484-chr8:99117612..99122860,5	MCF-7	breast:
21	chr8:99056634..99059248-chr8:99059651..99063296,8	MCF-7	breast:
22	chr16:769309..771169-chr8:99056941..99058600,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-703P	TF binding region
RPL30	TF binding region
SNORA72	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000085719	Chromatin interaction
ENSG00000104361	Chromatin interaction
ENSG00000176623	Chromatin interaction
ENSG00000104341	Chromatin interaction
ENSG00000132561	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000104356	Chromatin interaction
ENSG00000252755	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000272993	Chromatin interaction
ENSG00000008282	Chromatin interaction
ENSG00000132541	Chromatin interaction
ENSG00000168140	Chromatin interaction
ENSG00000270682	Chromatin interaction
ENSG00000147649	Chromatin interaction
ENSG00000103254	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10098159	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs10955141	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955142	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955145	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955146	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955147	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11559201	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11559202	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11775531	0.87[ASW][hapmap];0.93[YRI][hapmap]
rs11776602	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784449	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785807	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11990341	0.83[ASN][1000 genomes]
rs11991161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11996042	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11997426	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12544193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549967	1.00[ASN][1000 genomes]
rs12550104	1.00[ASN][1000 genomes]
rs13248865	1.00[ASN][1000 genomes]
rs13254615	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254737	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265127	1.00[ASN][1000 genomes]
rs13268951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13269757	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13274382	1.00[ASN][1000 genomes]
rs13279197	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13439743	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17829645	1.00[JPT][hapmap]
rs2279120	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290469	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877453	0.87[ASW][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3088121	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34139241	1.00[ASN][1000 genomes]
rs34276726	1.00[ASN][1000 genomes]
rs34899856	1.00[ASN][1000 genomes]
rs35417638	1.00[ASN][1000 genomes]
rs3758031	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55698139	0.92[AFR][1000 genomes]
rs55779959	1.00[ASN][1000 genomes]
rs56137923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57866232	1.00[ASN][1000 genomes]
rs60324498	1.00[ASN][1000 genomes]
rs68116021	0.83[ASN][1000 genomes]
rs68131553	1.00[ASN][1000 genomes]
rs6985709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6986891	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987112	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004993	1.00[ASN][1000 genomes]
rs7012838	1.00[ASN][1000 genomes]
rs7016999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71514975	1.00[ASN][1000 genomes]
rs72678742	1.00[ASN][1000 genomes]
rs7835905	0.93[YRI][hapmap]
rs812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9918865	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13255477	LAPTM4B	cis	lymphoblastoid	seeQTL
rs13255477	DPY19L4	cis	cerebellum	SCAN
rs13255477	SPAG1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99055000-99059000	Active TSS	Right Ventricle	heart
2	chr8:99055200-99058600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:99055200-99059200	Active TSS	GM12878-XiMat	blood
4	chr8:99055800-99059000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:99056000-99059400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:99056200-99059000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr8:99056400-99058800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:99056400-99058800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr8:99056400-99058800	Active TSS	Lung	lung
10	chr8:99056400-99058800	Active TSS	Pancreas	Pancrea
11	chr8:99056400-99058800	Bivalent/Poised TSS	HepG2	liver
12	chr8:99056400-99059000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:99056400-99059000	Active TSS	Ovary	ovary
14	chr8:99056400-99059000	Active TSS	Right Atrium	heart
15	chr8:99056600-99058400	Active TSS	Colonic Mucosa	Colon
16	chr8:99056600-99058600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr8:99056600-99058600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:99056600-99058800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:99056600-99058800	Active TSS	Fetal Intestine Large	intestine
20	chr8:99056600-99058800	Active TSS	Fetal Kidney	kidney
21	chr8:99056600-99058800	Active TSS	Left Ventricle	heart
22	chr8:99056600-99059000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:99056600-99059000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr8:99056600-99059000	Active TSS	Psoas Muscle	Psoas
25	chr8:99056800-99058400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr8:99056800-99058400	Active TSS	Fetal Muscle Trunk	muscle
27	chr8:99056800-99058400	Active TSS	Placenta	Placenta
28	chr8:99056800-99058400	Active TSS	Fetal Thymus	thymus
29	chr8:99056800-99058400	Active TSS	NH-A	brain
30	chr8:99056800-99058600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr8:99056800-99058600	Active TSS	Fetal Heart	heart
32	chr8:99056800-99058600	Active TSS	HSMM	muscle
33	chr8:99056800-99058800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr8:99056800-99058800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:99056800-99058800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr8:99056800-99058800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr8:99056800-99058800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:99056800-99058800	Active TSS	Esophagus	oesophagus
39	chr8:99056800-99058800	Active TSS	Fetal Intestine Small	intestine
40	chr8:99056800-99058800	Active TSS	Gastric	stomach
41	chr8:99056800-99058800	Active TSS	Placenta Amnion	Placenta Amnion
42	chr8:99056800-99059000	Active TSS	H9 Cell Line	embryonic stem cell
43	chr8:99056800-99059000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:99056800-99059200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr8:99056800-99059200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:99056800-99059200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr8:99056800-99059400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr8:99057000-99058400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr8:99057000-99058400	Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr8:99057000-99058400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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