Variant report

Variant	rs11998387
Chromosome Location	chr8:110655337-110655338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr8:110654793-110655649	K562	blood:	n/a	n/a
2	BHLHE40	chr8:110654773-110655762	K562	blood:	n/a	n/a
3	JUND	chr8:110654848-110655648	K562	blood:	n/a	chr8:110655457-110655465
4	IRF1	chr8:110655201-110655463	K562	blood:	n/a	n/a
5	CUX1	chr8:110655091-110655788	K562	blood:	n/a	n/a
6	TAL1	chr8:110655015-110655635	K562	blood:	n/a	n/a
7	EP300	chr8:110654913-110655596	K562	blood:	n/a	n/a
8	MAX	chr8:110654743-110657818	HCT-116	colon:	n/a	chr8:110655359-110655370 chr8:110657086-110657097 chr8:110655794-110655803 chr8:110657087-110657096 chr8:110657086-110657096 chr8:110657086-110657096 chr8:110656320-110656329
9	TBP	chr8:110654858-110655531	K562	blood:	n/a	n/a
10	GATA1	chr8:110655124-110655595	PBDE	blood:	n/a	chr8:110655292-110655299 chr8:110655291-110655301 chr8:110655292-110655299 chr8:110655292-110655299
11	STAT5A	chr8:110655064-110655520	K562	blood:	n/a	chr8:110655245-110655268 chr8:110655241-110655255
12	STAT5A	chr8:110654952-110655545	K562	blood:	n/a	chr8:110655245-110655268 chr8:110655241-110655255
13	YY1	chr8:110655287-110656140	GM12878	blood:	n/a	n/a
14	CHD2	chr8:110655275-110655579	GM12878	blood:	n/a	n/a
15	YY1	chr8:110655307-110655639	K562	blood:	n/a	n/a
16	RCOR1	chr8:110654774-110655626	K562	blood:	n/a	n/a
17	WRNIP1	chr8:110654833-110655600	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr8:110654942-110655664	K562	blood:	n/a	n/a
19	ZNF263	chr8:110654963-110657165	HEK293-T-REx	kidney:	n/a	n/a
20	STAT3	chr8:110655297-110655544	MCF10A-Er-Src	breast:	n/a	n/a
21	ZNF384	chr8:110654857-110655340	K562	blood:	n/a	n/a
22	MAX	chr8:110654773-110655523	K562	blood:	n/a	chr8:110655359-110655370
23	NR2F2	chr8:110655136-110655505	K562	blood:	n/a	n/a
24	ATF1	chr8:110654872-110655594	K562	blood:	n/a	n/a
25	IRF1	chr8:110655267-110655536	K562	blood:	n/a	n/a
26	MAZ	chr8:110654841-110655522	K562	blood:	n/a	chr8:110655359-110655370
27	MXI1	chr8:110655267-110655467	GM12878	blood:	n/a	n/a
28	MYC	chr8:110654826-110655615	K562	blood:	n/a	chr8:110655359-110655370
29	CTCF	chr8:110654744-110655488	K562	blood:	n/a	chr8:110654928-110654937 chr8:110654905-110654913
30	UBTF	chr8:110654952-110655588	K562	blood:	n/a	n/a
31	IKZF1	chr8:110655122-110655613	GM12878	blood:	n/a	chr8:110655502-110655510
32	ARID3A	chr8:110655021-110655482	K562	blood:	n/a	n/a
33	KAP1	chr8:110655314-110656850	HEK293	kidney:	n/a	n/a
34	MYC	chr8:110655295-110655504	K562	blood:	n/a	chr8:110655359-110655370
35	MYC	chr8:110655318-110655683	MCF10A-Er-Src	breast:	n/a	chr8:110655359-110655370
36	FOS	chr8:110655316-110655516	MCF10A-Er-Src	breast:	n/a	chr8:110655457-110655465
37	RCOR1	chr8:110654778-110655666	K562	blood:	n/a	n/a
38	JUN	chr8:110655236-110655543	K562	blood:	n/a	chr8:110655457-110655465
39	MAX	chr8:110654774-110655595	K562	blood:	n/a	chr8:110655359-110655370
40	TEAD4	chr8:110654776-110655736	K562	blood:	n/a	n/a
41	MAX	chr8:110654633-110655875	HCT-116	colon:	n/a	chr8:110655359-110655370 chr8:110655794-110655803
42	MYC	chr8:110654773-110655582	K562	blood:	n/a	chr8:110655359-110655370

No.	Distal block	Cell Line	Cell type
1	chr8:110344899..110348479-chr8:110652629..110655762,4	MCF-7	breast:
2	chr8:110551215..110554146-chr8:110654892..110657586,2	K562	blood:
3	chr8:110343048..110346506-chr8:110655063..110657604,4	MCF-7	breast:
4	chr8:110649169..110652040-chr8:110653790..110655530,2	K562	blood:
5	chr8:110550857..110553602-chr8:110653501..110657228,5	K562	blood:

Variant related genes	Relation type
ENSG00000248050	TF binding region
ENSG00000120526	Chromatin interaction
ENSG00000147654	Chromatin interaction
ENSG00000120533	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10090145	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505131	0.85[JPT][hapmap]
rs10505132	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11774663	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13256586	0.97[ASN][1000 genomes]
rs13268243	0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1573853	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3108829	0.89[ASN][1000 genomes]
rs3108832	0.88[ASN][1000 genomes]
rs3108837	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3108840	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3108853	0.90[ASN][1000 genomes]
rs3108854	0.90[ASN][1000 genomes]
rs3108862	0.91[ASN][1000 genomes]
rs3108865	0.91[ASN][1000 genomes]
rs3108869	0.90[ASN][1000 genomes]
rs3133926	0.87[ASN][1000 genomes]
rs3133927	0.89[ASN][1000 genomes]
rs3133935	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3133936	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3133937	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3134314	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3134317	0.91[ASN][1000 genomes]
rs3134319	0.91[ASN][1000 genomes]
rs3134325	0.89[ASN][1000 genomes]
rs3134331	0.89[ASN][1000 genomes]
rs6469275	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6985646	0.99[ASN][1000 genomes]
rs7008447	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][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	esv1849702	chr8:110594148-110683804	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11998387	KCNV1	cis	lymphoblastoid	seeQTL
rs11998387	PKHD1L1	cis	lymphoblastoid	seeQTL
rs11998387	PKHD1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:110633200-110656000	Weak transcription	Gastric	stomach
2	chr8:110643800-110655400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr8:110648200-110655600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr8:110650600-110655600	Weak transcription	Right Atrium	heart
5	chr8:110650600-110656200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr8:110651200-110655600	Weak transcription	Fetal Intestine Small	intestine
7	chr8:110652400-110655400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:110652400-110655400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr8:110652800-110655800	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:110653000-110655600	Weak transcription	A549	lung
11	chr8:110653400-110655400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr8:110653600-110656000	Weak transcription	Psoas Muscle	Psoas
13	chr8:110653800-110655400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:110654000-110656200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr8:110654600-110655400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:110654600-110655600	Enhancers	Fetal Brain Male	brain
17	chr8:110654800-110655400	Flanking Active TSS	Liver	Liver
18	chr8:110654800-110655600	Enhancers	Esophagus	oesophagus
19	chr8:110654800-110656200	Active TSS	Fetal Brain Female	brain
20	chr8:110654800-110656400	Active TSS	GM12878-XiMat	blood
21	chr8:110654800-110661200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr8:110655000-110655400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr8:110655000-110655600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:110655000-110655800	Enhancers	Primary B cells from peripheral blood	blood
25	chr8:110655000-110655800	Enhancers	Stomach Mucosa	stomach
26	chr8:110655000-110656200	Flanking Active TSS	HepG2	liver
27	chr8:110655000-110656800	Flanking Active TSS	K562	blood
28	chr8:110655000-110657600	Active TSS	Brain Anterior Caudate	brain
29	chr8:110655000-110657800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:110655200-110655400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr8:110655200-110655400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr8:110655200-110655400	Flanking Active TSS	HMEC	breast
33	chr8:110655200-110655400	Enhancers	NHEK	skin
34	chr8:110655200-110655400	Bivalent Enhancer	NHLF	lung
35	chr8:110655200-110655800	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:110655200-110656000	Enhancers	Brain Substantia Nigra	brain
37	chr8:110655200-110656000	Weak transcription	Lung	lung
38	chr8:110655200-110656000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
39	chr8:110655200-110656000	Flanking Active TSS	Hela-S3	cervix
40	chr8:110655200-110656200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr8:110655200-110656800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr8:110655200-110657800	Active TSS	Pancreas	Pancrea
43	chr8:110655200-110661200	Active TSS	Brain Angular Gyrus	brain

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