Variant report

Variant	rs12440601
Chromosome Location	chr15:50649601-50649602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50648747-50649607	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:50649591-50650280	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:50643941-50650733	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:50648646-50650254	GM12892	blood:	n/a	n/a
5	HEY1	chr15:50649332-50649817	K562	blood:	n/a	n/a
6	POLR2A	chr15:50649600-50649716	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr15:50645476-50650223	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:50649265-50649625	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr15:50649426-50649941	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:50645530-50650223	K562	blood:	n/a	n/a
11	POLR2A	chr15:50648531-50650361	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr15:50645808-50650538	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr15:50649541-50650154	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:50649565-50649898	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr15:50649401-50649705	ProgFib	skin:	n/a	n/a
16	POLR2A	chr15:50645464-50650252	K562	blood:	n/a	n/a
17	POLR2A	chr15:50649370-50649605	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:50646787-50650247	K562	blood:	n/a	n/a
19	POLR2A	chr15:50648927-50650213	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:50649091-50650143	HepG2	liver:	n/a	n/a
21	POLR2A	chr15:50648648-50650323	SK-N-MC	brain:	n/a	n/a
22	CHD1	chr15:50645052-50649822	IMR90	lung:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
23	POLR2A	chr15:50648702-50650294	MCF-7	breast:	n/a	n/a
24	POLR2A	chr15:50648563-50649654	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr15:50648710-50650269	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:50649544-50650301	GM12892	blood:	n/a	n/a
27	MXI1	chr15:50644670-50649694	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr15:50643912-50651678	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr15:50648713-50650325	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr15:50643981-50656245	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr15:50649534-50649928	K562	blood:	n/a	n/a
32	POLR2A	chr15:50648495-50649703	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr15:50649579-50649868	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:50646088-50651672	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr15:50649015-50650260	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr15:50648818-50650254	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr15:50644838-50649712	IMR90	lung:	n/a	n/a
38	POLR2A	chr15:50645312-50650230	GM12878	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50645594..50649830-chr15:50754186..50757976,9	MCF-7	breast:
2	chr15:50643045..50650563-chr15:50756489..50761004,9	MCF-7	breast:
3	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
4	chr15:50647163..50649970-chr15:50707470..50713022,5	MCF-7	breast:
5	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
6	chr15:50647220..50649637-chr15:50708002..50709799,2	K562	blood:
7	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
8	chr15:50646468..50650762-chr15:50786083..50789645,4	K562	blood:
9	chr15:50649293..50650992-chr15:50796880..50798462,2	K562	blood:
10	chr15:50649363..50652046-chr15:51189573..51192655,3	MCF-7	breast:
11	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
12	chr15:50547608..50550414-chr15:50649423..50651512,2	K562	blood:
13	chr15:50473027..50474535-chr15:50649075..50650577,2	K562	blood:
14	chr15:50648981..50650739-chr15:50748279..50750873,2	K562	blood:
15	chr15:50649548..50651206-chr15:50787408..50790314,2	MCF-7	breast:
16	chr15:50644601..50650486-chr15:50714318..50720349,10	K562	blood:
17	chr15:50644770..50653815-chr15:50713287..50720249,51	MCF-7	breast:
18	chr15:50646196..50649637-chr15:50705519..50710625,4	K562	blood:
19	chr15:50647970..50649936-chr15:50757455..50759138,2	K562	blood:
20	chr15:50648117..50650493-chr15:50779482..50782033,2	K562	blood:
21	chr15:50649460..50650988-chr15:50701227..50703885,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP8-2	chr15:50648297-50650501	ENSG00000244879
2	lnc-USP8-2	chr15:50646371-50650503	NONHSAT042406
3	lnc-USP8-2	chr15:50648297-50650501	NONHSAT042411
4	lnc-USP8-2	chr15:50648297-50650527	ENSG00000244879.2

No data

Variant related genes	Relation type
MIR4712	TF binding region
GABPB1	TF binding region
ENSG00000104043	Chromatin interaction
ENSG00000259618	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000242737	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 24 )

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

rs_ID	r²[population]
rs1056681	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070770	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070772	1.00[ASN][1000 genomes]
rs11855995	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857071	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903381	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909202	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917303	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509458	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598020	1.00[ASN][1000 genomes]
rs2013885	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013888	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2033114	1.00[ASN][1000 genomes]
rs2414049	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450641	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45508400	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504781	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022563	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022564	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022565	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022567	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022569	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62022570	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493426	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677143	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71424053	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72738935	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738949	0.82[EUR][1000 genomes]
rs8034849	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920021	1.00[ASN][1000 genomes]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs12440601	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs12440601	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12440601	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs12440601	GABPB1-AS1	cis	Heart Left Ventricle	GTEx
rs12440601	GABPB1-AS1	cis	Artery Tibial	GTEx
rs12440601	GABPB1-AS1	cis	Thyroid	GTEx
rs12440601	GABPB1-AS1	cis	Esophagus Muscularis	GTEx
rs12440601	GABPB1-AS1	cis	Artery Aorta	GTEx
rs12440601	CTD-3110H11.1	cis	Thyroid	GTEx
rs12440601	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs12440601	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs12440601	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs12440601	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs12440601	GABPB2	Cis_1M	lymphoblastoid	RTeQTL
rs12440601	CTD-3110H11.1	cis	lung	GTEx
rs12440601	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs12440601	GABPB1-AS1	cis	Muscle Skeletal	GTEx
rs12440601	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs12440601	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs12440601	GABPB1-AS1	cis	Whole Blood	GTEx
rs12440601	GABPB1-AS1	cis	Stomach	GTEx
rs12440601	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs12440601	CTD-3110H11.1	cis	Stomach	GTEx
rs12440601	GABPB1-AS1	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50644600-50649800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:50647800-50649800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:50648000-50667600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:50648200-50650000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr15:50648200-50653800	Weak transcription	Pancreas	Pancrea
6	chr15:50648200-50657200	Weak transcription	Esophagus	oesophagus
7	chr15:50648200-50658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:50648200-50664400	Weak transcription	Lung	lung
9	chr15:50648400-50650000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:50648400-50651200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:50648400-50652800	Weak transcription	Ovary	ovary
12	chr15:50648400-50660400	Weak transcription	Aorta	Aorta
13	chr15:50648600-50649800	Enhancers	Small Intestine	intestine
14	chr15:50648600-50650000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
15	chr15:50648600-50650000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr15:50648600-50650000	Transcr. at gene 5' and 3'	A549	lung
17	chr15:50648600-50650200	Enhancers	Spleen	Spleen
18	chr15:50648800-50649800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
19	chr15:50648800-50649800	Transcr. at gene 5' and 3'	Dnd41	blood
20	chr15:50648800-50649800	Flanking Active TSS	HepG2	liver
21	chr15:50648800-50650200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:50648800-50655600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:50649000-50649800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:50649000-50649800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:50649000-50649800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:50649000-50649800	Genic enhancers	Liver	Liver
27	chr15:50649000-50650000	Enhancers	Fetal Heart	heart
28	chr15:50649000-50650000	Enhancers	Placenta	Placenta
29	chr15:50649000-50650200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr15:50649000-50651400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:50649000-50651600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:50649000-50653400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr15:50649000-50658600	Weak transcription	Right Atrium	heart
34	chr15:50649200-50649800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
35	chr15:50649200-50649800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:50649200-50649800	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:50649200-50650000	Enhancers	Fetal Brain Male	brain
38	chr15:50649200-50652400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:50649200-50656400	Strong transcription	Fetal Muscle Leg	muscle
40	chr15:50649200-50664400	Weak transcription	Right Ventricle	heart
41	chr15:50649400-50649800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr15:50649400-50649800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:50649400-50649800	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr15:50649400-50649800	Genic enhancers	Fetal Lung	lung
45	chr15:50649400-50650000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:50649400-50650000	Genic enhancers	Fetal Thymus	thymus
47	chr15:50649400-50650200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:50649400-50650200	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr15:50649400-50650200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr15:50649400-50650200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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