Variant report

Variant	rs2298058
Chromosome Location	chr13:95248566-95248567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:409)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:409 , 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	ZKSCAN1	chr13:95248300-95248612	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr13:95248174-95248764	PFSK-1	brain:	n/a	n/a
3	ELF1	chr13:95248295-95248756	A549	lung:	n/a	chr13:95248667-95248678
4	NRF1	chr13:95248077-95248790	GM12878	blood:	n/a	chr13:95248583-95248592 chr13:95248583-95248594 chr13:95248582-95248593 chr13:95248583-95248597
5	POLR2A	chr13:95247654-95248807	HUVEC	blood vessel:	n/a	n/a
6	NRF1	chr13:95248395-95248762	HepG2	liver:	n/a	chr13:95248583-95248592 chr13:95248583-95248594 chr13:95248582-95248593 chr13:95248583-95248597
7	TAF1	chr13:95248131-95248756	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr13:95248115-95248784	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr13:95248424-95248657	A549	lung:	n/a	n/a
10	FOS	chr13:95248466-95248578	MCF10A-Er-Src	breast:	n/a	n/a
11	TAF1	chr13:95247908-95249042	ECC-1	luminal epithelium:	n/a	n/a
12	CHD2	chr13:95247696-95248746	GM12878	blood:	n/a	n/a
13	REST	chr13:95248088-95248750	A549	lung:	n/a	n/a
14	POLR2A	chr13:95247992-95248832	HUVEC	blood vessel:	n/a	n/a
15	MYBL2	chr13:95248195-95248830	HepG2	liver:	n/a	n/a
16	TAF1	chr13:95248097-95248690	GM12892	blood:	n/a	n/a
17	POLR2A	chr13:95247296-95248835	Hela-S3	cervix:	n/a	n/a
18	SP1	chr13:95248207-95248689	GM12878	blood:	n/a	chr13:95248560-95248572 chr13:95248561-95248570 chr13:95248560-95248572 chr13:95248562-95248571
19	SIN3AK20	chr13:95248182-95248593	K562	blood:	n/a	n/a
20	HEY1	chr13:95248106-95248835	HepG2	liver:	n/a	chr13:95248556-95248571
21	NRF1	chr13:95248379-95248791	H1-hESC	embryonic stem cell:	n/a	chr13:95248583-95248592 chr13:95248583-95248594 chr13:95248582-95248593 chr13:95248583-95248597
22	POLR2A	chr13:95247921-95248801	K562	blood:	n/a	n/a
23	POU2F2	chr13:95247931-95248699	GM12891	blood:	n/a	n/a
24	EP300	chr13:95248308-95248852	K562	blood:	n/a	n/a
25	TAF1	chr13:95248206-95248663	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr13:95248206-95248806	HepG2	liver:	n/a	n/a
27	REST	chr13:95248158-95248779	H1-neurons	neurons:	n/a	n/a
28	HEY1	chr13:95248161-95248707	HepG2	liver:	n/a	chr13:95248556-95248571
29	POLR2A	chr13:95247191-95249090	HepG2	liver:	n/a	n/a
30	CEBPB	chr13:95248101-95248745	GM12878	blood:	n/a	n/a
31	POLR2A	chr13:95248149-95248802	PFSK-1	brain:	n/a	n/a
32	UBTF	chr13:95248146-95248617	K562	blood:	n/a	n/a
33	ELF1	chr13:95248196-95248897	GM12878	blood:	n/a	chr13:95248667-95248678
34	REST	chr13:95248124-95248601	HepG2	liver:	n/a	n/a
35	SMARCB1	chr13:95247859-95248766	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr13:95247256-95248844	HEK293	kidney:	n/a	n/a
37	POLR2A	chr13:95247877-95248801	K562	blood:	n/a	n/a
38	CTCF	chr13:95248500-95248650	AG04449	skin:	n/a	n/a
39	POLR2A	chr13:95247398-95248823	HepG2	liver:	n/a	n/a
40	TAF1	chr13:95247967-95248807	A549	lung:	n/a	n/a
41	POLR2A	chr13:95247223-95248837	PBDE	blood:	n/a	n/a
42	ZNF263	chr13:95247830-95248618	HEK293-T-REx	kidney:	n/a	n/a
43	HMGN3	chr13:95248193-95248976	K562	blood:	n/a	n/a
44	MAZ	chr13:95247880-95248744	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr13:95248139-95248707	GM12891	blood:	n/a	n/a
46	TBP	chr13:95248029-95248752	GM12878	blood:	n/a	n/a
47	POU2F2	chr13:95248154-95248792	GM12878	blood:	n/a	n/a
48	CTCF	chr13:95248480-95248630	SAEC	small airway:	n/a	n/a
49	POLR2A	chr13:95247908-95248741	Hela-S3	cervix:	n/a	n/a
50	ATF3	chr13:95248221-95248684	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:95248547-95248597	PrEC	prostate:	n/a
2	chr13:95248547-95248597	BE2_C	brain:	n/a
3	chr13:95248547-95248597	RPTEC	kidney:	n/a
4	chr13:95248547-95248597	GM12892	blood:	n/a
5	chr13:95248547-95248597	ovcar-3	ovarian:	n/a
6	chr13:95248547-95248597	GM19239	blood:	n/a
7	chr13:95248547-95248597	SKMC	muscle:	n/a
8	chr13:95248547-95248597	NH-A	brain:	n/a
9	chr13:95248547-95248597	GM12891	blood:	n/a
10	chr13:95248547-95248597	HEK293	kidney:	embryo
11	chr13:95248547-95248597	HRE	kidney:	n/a
12	chr13:95248547-95248597	HNPCEpiC	eye:	n/a
13	chr13:95248547-95248597	ProgFib	skin:	n/a
14	chr13:95248547-95248597	K562	blood:	n/a
15	chr13:95248547-95248597	BJ	skin:	n/a
16	chr13:95248547-95248597	HRPEpiC	eye:	n/a
17	chr13:95248547-95248597	SK-N-SH_RA	brain:	n/a
18	chr13:95248547-95248597	H1-hESC	embryonic stem cell:	embryo
19	chr13:95248547-95248597	HCM	heart:	n/a
20	chr13:95248547-95248597	LNCaP	prostate:	n/a
21	chr13:95248547-95248597	SK-N-MC	brain:	n/a
22	chr13:95248547-95248597	SAEC	small airway:	n/a
23	chr13:95248547-95248597	MCF10A-Er-Src	breast:	n/a
24	chr13:95248547-95248597	AoSMC	blood vessel:	n/a
25	chr13:95248547-95248597	AG10803	skin:	n/a
26	chr13:95248547-95248597	GM06990	blood:	n/a
27	chr13:95248547-95248597	Jurkat	blood:	n/a
28	chr13:95248547-95248597	HepG2	liver:	n/a
29	chr13:95248547-95248597	HPAEpiC	pulmonary alveolar:	n/a
30	chr13:95248547-95248597	AG09309	skin:	n/a
31	chr13:95248547-95248597	NT2-D1	testis:	n/a
32	chr13:95248547-95248597	ECC-1	luminal epithelium:	n/a
33	chr13:95248547-95248597	Hepatocyte	liver:	n/a
34	chr13:95248547-95248597	GM12878	blood:	n/a
35	chr13:95248547-95248597	MCF-7	breast:	n/a
36	chr13:95248547-95248597	HEEpiC	esophagus:	n/a
37	chr13:95248547-95248597	T-47D	breast:	n/a
38	chr13:95248547-95248597	IMR90	lung:	fetal
39	chr13:95248547-95248597	HCF	heart:	n/a
40	chr13:95248547-95248597	HAEpiC	amniotic membrane:	n/a
41	chr13:95248547-95248597	U87	brain:	n/a
42	chr13:95248547-95248597	HIPEpiC	eye:	n/a
43	chr13:95248547-95248597	AG04450	lung:	fetal
44	chr13:95248547-95248597	AG04449	skin:	fetal
45	chr13:95248547-95248597	NB4	blood:	n/a
46	chr13:95248547-95248597	HRCEpiC	kidney:	n/a
47	chr13:95248547-95248597	HUVEC	blood vessel:	n/a
48	chr13:95248547-95248597	A549	lung:	n/a
49	chr13:95248547-95248597	HMEC	breast:	n/a
50	chr13:95248547-95248597	PANC-1	pancreas:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr13:95248444..95249010-chr19:47291436..47292069,2	NB4	blood:
2	chr13:95247274..95249727-chr13:95251841..95255221,4	MCF-7	breast:
3	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:
4	chr11:62358993..62359769-chr13:95247964..95248584,2	NB4	blood:
5	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
6	chr13:95247805..95248577-chr20:30192835..30193557,2	Hela-S3	cervix:
7	chr13:95247949..95248595-chr17:2206672..2207436,2	NB4	blood:

No data

Variant related genes	Relation type
TGDS	TF binding region
TGDS	CpG island
ENSG00000125968	Chromatin interaction
ENSG00000070366	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000167720	Chromatin interaction
ENSG00000105281	Chromatin interaction
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1112370	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1408999	0.94[ASN][1000 genomes]
rs2275647	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275648	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34350725	0.97[ASN][1000 genomes]
rs34405130	0.97[ASN][1000 genomes]
rs35678857	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742107	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4473052	0.94[ASN][1000 genomes]
rs4489873	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4608209	0.94[ASN][1000 genomes]
rs4773801	0.97[ASN][1000 genomes]
rs6492716	0.97[ASN][1000 genomes]
rs6492717	0.88[ASN][1000 genomes]
rs6492718	0.97[ASN][1000 genomes]
rs6492720	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492721	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7321239	0.97[ASN][1000 genomes]
rs7330873	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7331814	0.96[ASN][1000 genomes]
rs7339106	0.97[ASN][1000 genomes]
rs7991607	0.97[ASN][1000 genomes]
rs7997035	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7997333	0.97[ASN][1000 genomes]
rs7998025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9301979	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9301981	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9301983	0.98[ASN][1000 genomes]
rs9516434	0.83[ASN][1000 genomes]
rs9516437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9516438	0.96[ASN][1000 genomes]
rs9516440	0.98[ASN][1000 genomes]
rs9516441	0.95[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs9524545	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524547	0.96[ASN][1000 genomes]
rs9524548	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524549	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524550	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524551	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9524553	0.98[ASN][1000 genomes]
rs9524554	0.98[ASN][1000 genomes]
rs9556402	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9556403	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556404	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9561638	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561642	0.98[ASN][1000 genomes]
rs9561643	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9590037	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3521585	chr13:95244823-95249508	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
5	esv3497281	chr13:95244835-95249503	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
6	esv3497282	chr13:95244837-95249504	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
7	esv3521596	chr13:95244837-95249504	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2298058	GPR180	cis	multi-tissue	Pritchard
rs2298058	GPR180	cis	lung	GTEx
rs2298058	GPR180	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95246200-95248600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:95246400-95249000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr13:95246400-95249000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:95246800-95249000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:95247000-95248800	Active TSS	GM12878-XiMat	blood
6	chr13:95247000-95249000	Active TSS	K562	blood
7	chr13:95247200-95248600	Active TSS	Fetal Brain Male	brain
8	chr13:95247200-95248600	Active TSS	NHLF	lung
9	chr13:95247200-95248800	Active TSS	Lung	lung
10	chr13:95247200-95249000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr13:95247400-95248800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:95247400-95248800	Active TSS	Aorta	Aorta
13	chr13:95247400-95248800	Active TSS	Fetal Intestine Small	intestine
14	chr13:95247400-95248800	Active TSS	Fetal Muscle Trunk	muscle
15	chr13:95247400-95248800	Active TSS	Gastric	stomach
16	chr13:95247400-95248800	Active TSS	Stomach Mucosa	stomach
17	chr13:95247400-95249000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:95247400-95249000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr13:95247400-95249000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr13:95247400-95249000	Active TSS	A549	lung
21	chr13:95247400-95249200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr13:95247600-95248600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:95247600-95248800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:95247600-95248800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:95247600-95248800	Active TSS	Esophagus	oesophagus
26	chr13:95247600-95248800	Active TSS	Fetal Heart	heart
27	chr13:95247600-95248800	Active TSS	Thymus	Thymus
28	chr13:95247600-95248800	Active TSS	NHDF-Ad	bronchial
29	chr13:95247600-95249000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr13:95247600-95249000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:95247600-95249000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr13:95247600-95249000	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr13:95247600-95249000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr13:95247600-95249000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:95247600-95249000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:95247600-95249000	Active TSS	Brain Hippocampus Middle	brain
37	chr13:95247600-95249000	Active TSS	Fetal Intestine Large	intestine
38	chr13:95247600-95249000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr13:95247600-95249000	Active TSS	Placenta Amnion	Placenta Amnion
40	chr13:95247600-95249000	Active TSS	Rectal Smooth Muscle	rectum
41	chr13:95247600-95249000	Active TSS	Right Atrium	heart
42	chr13:95247600-95249200	Active TSS	Colonic Mucosa	Colon
43	chr13:95247600-95249200	Active TSS	NHEK	skin
44	chr13:95247800-95248600	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr13:95247800-95248600	Active TSS	Spleen	Spleen
46	chr13:95247800-95248600	Active TSS	Dnd41	blood
47	chr13:95247800-95248800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr13:95247800-95248800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:95247800-95248800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:95247800-95248800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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