Variant report

Variant	rs12289223
Chromosome Location	chr11:18610857-18610858
allele	C/G
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	SMARCC1	chr11:18609697-18611092	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:18609667-18610972	HepG2	liver:	n/a	n/a
3	USF2	chr11:18610274-18611012	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr11:18609353-18611058	IMR90	lung:	n/a	n/a
5	HCFC1	chr11:18609334-18611019	Hela-S3	cervix:	n/a	n/a
6	MYC	chr11:18609829-18610916	NB4	blood:	n/a	chr11:18610553-18610560
7	RELA	chr11:18610046-18610869	GM19099	blood:	n/a	n/a
8	TCF12	chr11:18609980-18611030	ECC-1	luminal epithelium:	n/a	chr11:18610034-18610044
9	MYC	chr11:18609442-18610876	K562	blood:	n/a	chr11:18610553-18610560
10	SIN3A	chr11:18609465-18610909	H1-hESC	embryonic stem cell:	n/a	chr11:18610354-18610367 chr11:18610356-18610367 chr11:18610366-18610379
11	POLR2A	chr11:18609427-18611144	Hela-S3	cervix:	n/a	n/a
12	EP300	chr11:18610044-18611025	K562	blood:	n/a	chr11:18610363-18610379 chr11:18610354-18610370
13	SMC3	chr11:18609621-18611079	Hela-S3	cervix:	n/a	chr11:18609935-18609949
14	MAX	chr11:18609725-18610964	HCT-116	colon:	n/a	chr11:18610553-18610560
15	POLR2A	chr11:18609366-18610926	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:18609350-18610878	HUVEC	blood vessel:	n/a	n/a
17	MAZ	chr11:18609747-18610994	IMR90	lung:	n/a	chr11:18610553-18610560
18	MAX	chr11:18609700-18610909	K562	blood:	n/a	chr11:18610553-18610560
19	JUND	chr11:18609920-18610997	K562	blood:	n/a	n/a
20	MAX	chr11:18610215-18610923	H1-hESC	embryonic stem cell:	n/a	chr11:18610553-18610560
21	REST	chr11:18609760-18610913	A549	lung:	n/a	chr11:18610351-18610364
22	BRCA1	chr11:18609896-18610869	Hela-S3	cervix:	n/a	n/a
23	MAX	chr11:18609320-18611078	A549	lung:	n/a	chr11:18610553-18610560
24	MXI1	chr11:18609362-18611188	SK-N-SH	brain:	n/a	n/a
25	RCOR1	chr11:18609501-18611412	K562	blood:	n/a	n/a
26	GABPA	chr11:18609811-18610870	MCF-7	breast:	n/a	n/a
27	ELF1	chr11:18609743-18610910	HCT-116	colon:	n/a	chr11:18610352-18610364 chr11:18610248-18610261
28	REST	chr11:18609319-18610920	H1-neurons	neurons:	n/a	chr11:18610351-18610364
29	SIN3AK20	chr11:18609666-18610903	HCT-116	colon:	n/a	n/a
30	RELA	chr11:18609238-18610896	GM12891	blood:	n/a	n/a
31	ZNF384	chr11:18610134-18611011	K562	blood:	n/a	n/a
32	TCF7L2	chr11:18609843-18611044	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18599363..18605712-chr11:18606522..18612149,6	MCF-7	breast:
2	chr11:18608525..18612049-chr11:18615119..18618882,10	MCF-7	breast:
3	chr11:18032918..18034516-chr11:18609753..18611706,2	MCF-7	breast:
4	chr11:18608840..18612225-chr11:18653403..18657833,8	MCF-7	breast:
5	chr11:18597269..18603847-chr11:18605648..18613112,11	MCF-7	breast:
6	chr11:18546303..18549278-chr11:18609985..18612598,2	K562	blood:
7	chr11:18609259..18612621-chr11:18654534..18657923,6	MCF-7	breast:
8	chr11:18608159..18612115-chr11:18615596..18618860,5	MCF-7	breast:
9	chr1:171454647..171455196-chr11:18610341..18611032,2	Hela-S3	cervix:
10	chr11:18547166..18549278-chr11:18610430..18612598,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UEVLD-1	chr11:18610405-18611827	NONHSAT018299
2	lnc-UEVLD-1	chr11:18610405-18611832	NONHSAT018300

Variant related genes	Relation type
UEVLD	TF binding region
ENSG00000117523	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000129158	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000256282	Chromatin interaction
ENSG00000151116	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10500835	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024669	0.85[EUR][1000 genomes]
rs11024677	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11024688	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024693	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11024706	0.90[TSI][hapmap]
rs11024714	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024715	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024725	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024726	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024727	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs11024728	0.87[ASN][1000 genomes]
rs12222154	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12418726	0.90[TSI][hapmap]
rs12421394	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12574333	0.86[TSI][hapmap]
rs16935541	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16935559	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16935575	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1979051	0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs1983124	0.95[JPT][hapmap]
rs2279900	0.86[TSI][hapmap]
rs2279902	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2291751	0.89[EUR][1000 genomes]
rs2292179	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2305166	0.90[TSI][hapmap]
rs3781640	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4436523	0.95[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs55969503	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61882886	0.85[EUR][1000 genomes]
rs61884673	0.91[EUR][1000 genomes]
rs61884715	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61884716	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61884723	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61884724	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61886140	0.88[EUR][1000 genomes]
rs61886141	0.88[EUR][1000 genomes]
rs6416020	0.82[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs7105387	0.83[ASN][1000 genomes]
rs72881309	0.87[ASN][1000 genomes]
rs7950602	0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	esv2761651	chr11:18606832-18621409	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12289223	LDHC	cis	parietal	SCAN
rs12289223	NUCB2	cis	cerebellum	SCAN
rs12289223	TSG101	cis	lymphoblastoid	seeQTL
rs12289223	UEVLD	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18608800-18611000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr11:18608800-18611000	Active TSS	Stomach Smooth Muscle	stomach
3	chr11:18608800-18611000	Active TSS	HSMMtube	muscle
4	chr11:18608800-18611400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:18608800-18612200	Active TSS	A549	lung
6	chr11:18609000-18611000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:18609000-18611000	Active TSS	Fetal Kidney	kidney
8	chr11:18609000-18611200	Active TSS	NHLF	lung
9	chr11:18609000-18611400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr11:18609000-18611400	Active TSS	Right Atrium	heart
11	chr11:18609000-18611400	Active TSS	NHDF-Ad	bronchial
12	chr11:18609000-18611800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr11:18609000-18611800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr11:18609000-18611800	Active TSS	Fetal Brain Female	brain
15	chr11:18609000-18612000	Active TSS	Colonic Mucosa	Colon
16	chr11:18609200-18611000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:18609200-18611000	Active TSS	Fetal Intestine Large	intestine
18	chr11:18609200-18611000	Active TSS	HMEC	breast
19	chr11:18609200-18611000	Active TSS	K562	blood
20	chr11:18609200-18611200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr11:18609200-18611200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:18609200-18611200	Active TSS	Thymus	Thymus
23	chr11:18609200-18611400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr11:18609200-18611400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:18609200-18611400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:18609200-18611400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr11:18609200-18611400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:18609200-18611400	Active TSS	GM12878-XiMat	blood
29	chr11:18609200-18612000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:18609200-18612000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr11:18609200-18612200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:18609400-18611000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:18609400-18611000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr11:18609400-18611000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:18609400-18611000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:18609400-18611000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr11:18609400-18611000	Active TSS	Aorta	Aorta
38	chr11:18609400-18611000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr11:18609400-18611000	Active TSS	Esophagus	oesophagus
40	chr11:18609400-18611000	Active TSS	Fetal Intestine Small	intestine
41	chr11:18609400-18611000	Active TSS	Fetal Stomach	stomach
42	chr11:18609400-18611000	Active TSS	Gastric	stomach
43	chr11:18609400-18611000	Active TSS	Right Ventricle	heart
44	chr11:18609400-18611000	Active TSS	Stomach Mucosa	stomach
45	chr11:18609400-18611000	Active TSS	HepG2	liver
46	chr11:18609400-18611000	Active TSS	Osteobl	bone
47	chr11:18609400-18611200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr11:18609400-18611200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr11:18609400-18611200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:18609400-18611200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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