Variant report

Variant	rs3897473
Chromosome Location	chr13:95253920-95253921
allele	G/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	POLR2A	chr13:95253845-95254644	GM12878	blood:	n/a	n/a
2	TEAD4	chr13:95253603-95254330	K562	blood:	n/a	n/a
3	CHD2	chr13:95253645-95254676	H1-hESC	embryonic stem cell:	n/a	chr13:95254336-95254346 chr13:95254123-95254133
4	MAX	chr13:95253535-95254741	H1-hESC	embryonic stem cell:	n/a	chr13:95254118-95254127
5	CEBPB	chr13:95253814-95253977	K562	blood:	n/a	n/a
6	MAX	chr13:95253513-95254791	A549	lung:	n/a	chr13:95253532-95253542 chr13:95254118-95254127
7	POLR2A	chr13:95253594-95254683	U87	brain:	n/a	n/a
8	E2F1	chr13:95253908-95254551	Hela-S3	cervix:	n/a	chr13:95254335-95254344 chr13:95254130-95254140 chr13:95254137-95254147 chr13:95254335-95254347 chr13:95254098-95254107
9	CBX3	chr13:95253512-95254519	K562	blood:	n/a	n/a
10	STAT3	chr13:95253731-95254141	MCF10A-Er-Src	breast:	n/a	chr13:95254098-95254110
11	RCOR1	chr13:95253792-95254522	K562	blood:	n/a	n/a
12	MXI1	chr13:95253560-95254781	IMR90	lung:	n/a	n/a
13	SMC3	chr13:95253815-95254100	Hela-S3	cervix:	n/a	n/a
14	MYC	chr13:95253677-95254136	MCF10A-Er-Src	breast:	n/a	chr13:95254118-95254127
15	POLR2A	chr13:95253799-95254896	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr13:95253802-95254718	Gliobla	brain:	n/a	n/a
17	POLR2A	chr13:95253684-95254692	GM15510	blood:	n/a	n/a
18	GABPA	chr13:95253655-95254374	MCF-7	breast:	n/a	chr13:95253846-95253860 chr13:95254335-95254344 chr13:95253837-95253851 chr13:95253846-95253857 chr13:95253843-95253857
19	UBTF	chr13:95253816-95254662	K562	blood:	n/a	n/a
20	POLR2A	chr13:95253904-95254350	GM12891	blood:	n/a	n/a
21	E2F6	chr13:95253565-95254228	K562	blood:	n/a	chr13:95254130-95254140 chr13:95254137-95254147 chr13:95253880-95253891 chr13:95254098-95254107
22	SP2	chr13:95253760-95254193	H1-hESC	embryonic stem cell:	n/a	chr13:95253936-95253951 chr13:95254053-95254063 chr13:95253993-95254008
23	MAX	chr13:95253531-95254484	MCF-7	breast:	n/a	chr13:95253532-95253542 chr13:95254118-95254127
24	MYC	chr13:95253677-95254682	NB4	blood:	n/a	chr13:95254118-95254127
25	MXI1	chr13:95253776-95255084	Hela-S3	cervix:	n/a	n/a
26	SP1	chr13:95253724-95254237	GM12878	blood:	n/a	chr13:95254097-95254106 chr13:95253993-95254004 chr13:95254097-95254107 chr13:95254097-95254111 chr13:95254096-95254108 chr13:95254098-95254107
27	POLR2A	chr13:95253621-95254718	PANC-1	pancreas:	n/a	n/a
28	PBX3	chr13:95253680-95254453	SK-N-SH	brain:	n/a	chr13:95254054-95254063
29	STAT3	chr13:95253730-95254103	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr13:95253915-95254613	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAX	chr13:95253616-95254087	GM12878	blood:	n/a	n/a
32	NFIC	chr13:95253493-95254161	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr13:95253605-95254665	Raji	blood:	n/a	n/a
34	TCF12	chr13:95253559-95254775	ECC-1	luminal epithelium:	n/a	chr13:95254567-95254574 chr13:95254074-95254084
35	NFYB	chr13:95253680-95254641	GM12878	blood:	n/a	chr13:95254054-95254064
36	MXI1	chr13:95253591-95255182	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr13:95253726-95254402	GM12878	blood:	n/a	n/a
38	POLR2A	chr13:95253709-95254659	HL-60	blood:	n/a	n/a
39	NRF1	chr13:95253653-95254041	H1-hESC	embryonic stem cell:	n/a	chr13:95253846-95253860 chr13:95253837-95253851 chr13:95253845-95253856 chr13:95253846-95253857 chr13:95253843-95253857
40	MAX	chr13:95253378-95254759	ECC-1	luminal epithelium:	n/a	chr13:95253532-95253542 chr13:95254118-95254127 chr13:95253492-95253502
41	FOXA1	chr13:95253828-95254102	T-47D	breast:	n/a	n/a
42	TAF1	chr13:95253784-95254299	SK-N-SH	brain:	n/a	n/a
43	FOS	chr13:95253852-95254187	GM12878	blood:	n/a	chr13:95254099-95254108
44	MAX	chr13:95253612-95254600	A549	lung:	n/a	chr13:95254118-95254127
45	MAX	chr13:95253543-95254686	HCT-116	colon:	n/a	chr13:95254118-95254127
46	SP1	chr13:95253648-95254501	A549	lung:	n/a	chr13:95254335-95254344 chr13:95254097-95254106 chr13:95253993-95254004 chr13:95254097-95254107 chr13:95254340-95254349 chr13:95254336-95254345 chr13:95254336-95254345 chr13:95254331-95254345 chr13:95254097-95254111 chr13:95254096-95254108 chr13:95254098-95254107 chr13:95254334-95254346
47	ARID3A	chr13:95253882-95254160	K562	blood:	n/a	n/a
48	CREB1	chr13:95253699-95254446	GM12878	blood:	n/a	n/a
49	SMARCB1	chr13:95253764-95254717	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr13:95253762-95254751	H1-neurons	neurons:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:95253900-95253950	NH-A	brain:	n/a
2	chr13:95253900-95253950	GM12878	blood:	n/a
3	chr13:95253900-95253950	HUVEC	blood vessel:	n/a
4	chr13:95253900-95253950	HIPEpiC	eye:	n/a
5	chr13:95253900-95253950	BJ	skin:	n/a
6	chr13:95253900-95253950	BE2_C	brain:	n/a
7	chr13:95253900-95253950	NB4	blood:	n/a
8	chr13:95253900-95253950	HRPEpiC	eye:	n/a
9	chr13:95253900-95253950	AG09319	gingival:	n/a
10	chr13:95253900-95253950	MCF-7	breast:	n/a
11	chr13:95253900-95253950	AG09309	skin:	n/a
12	chr13:95253900-95253950	IMR90	lung:	fetal
13	chr13:95253900-95253950	AG04449	skin:	fetal
14	chr13:95253900-95253950	HRE	kidney:	n/a
15	chr13:95253900-95253950	AG04450	lung:	fetal
16	chr13:95253900-95253950	MCF10A-Er-Src	breast:	n/a
17	chr13:95253900-95253950	AG10803	skin:	n/a
18	chr13:95253900-95253950	Caco-2	colon:	n/a
19	chr13:95253900-95253950	U87	brain:	n/a
20	chr13:95253900-95253950	SK-N-SH_RA	brain:	n/a
21	chr13:95253900-95253950	HEEpiC	esophagus:	n/a
22	chr13:95253900-95253950	A549	lung:	n/a
23	chr13:95253900-95253950	T-47D	breast:	n/a
24	chr13:95253900-95253950	LNCaP	prostate:	n/a
25	chr13:95253900-95253950	HCPEpiC	choroid plexus:	n/a
26	chr13:95253900-95253950	PrEC	prostate:	n/a
27	chr13:95253900-95253950	HCM	heart:	n/a
28	chr13:95253900-95253950	H1-hESC	embryonic stem cell:	embryo
29	chr13:95253900-95253950	SK-N-MC	brain:	n/a
30	chr13:95253900-95253950	Hela-S3	cervix:	n/a
31	chr13:95253900-95253950	HPAEpiC	pulmonary alveolar:	n/a
32	chr13:95253900-95253950	HNPCEpiC	eye:	n/a
33	chr13:95253900-95253950	PANC-1	pancreas:	n/a
34	chr13:95253900-95253950	HL-60	blood:	n/a
35	chr13:95253900-95253950	ovcar-3	ovarian:	n/a
36	chr13:95253900-95253950	CMK	blood:	n/a
37	chr13:95253900-95253950	GM12891	blood:	n/a
38	chr13:95253900-95253950	HepG2	liver:	n/a
39	chr13:95253900-95253950	K562	blood:	n/a
40	chr13:95253900-95253950	GM19239	blood:	n/a
41	chr13:95253900-95253950	NHDF-neo	bronchial:	n/a
42	chr13:95253900-95253950	AoSMC	blood vessel:	n/a
43	chr13:95253900-95253950	NHBE	bronchial:	n/a
44	chr13:95253900-95253950	HCF	heart:	n/a
45	chr13:95253900-95253950	PFSK-1	brain:	n/a
46	chr13:95253900-95253950	ProgFib	skin:	n/a
47	chr13:95253900-95253950	Hepatocyte	liver:	n/a
48	chr13:95253900-95253950	HRCEpiC	kidney:	n/a
49	chr13:95253900-95253950	SAEC	small airway:	n/a
50	chr13:95253900-95253950	NT2-D1	testis:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:95247274..95249727-chr13:95251841..95255221,4	MCF-7	breast:
2	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
3	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:

Variant related genes	Relation type
GPR180	TF binding region
GPR180	CpG island
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1112370	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1341267	0.90[ASN][1000 genomes]
rs1408999	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1572935	0.96[ASN][1000 genomes]
rs2275648	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2298055	0.91[ASN][1000 genomes]
rs2298056	0.90[ASN][1000 genomes]
rs2298057	0.91[ASN][1000 genomes]
rs34350725	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34405130	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35253817	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742107	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3897474	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238308	0.95[ASN][1000 genomes]
rs4296139	0.95[ASN][1000 genomes]
rs4465476	0.90[ASN][1000 genomes]
rs4473052	0.85[EUR][1000 genomes]
rs4608209	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4771890	0.91[ASN][1000 genomes]
rs4773801	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492716	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492718	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492720	0.99[ASN][1000 genomes]
rs6492721	0.98[ASN][1000 genomes]
rs6492723	0.95[ASN][1000 genomes]
rs6492725	0.90[ASN][1000 genomes]
rs7321239	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7326576	0.90[ASN][1000 genomes]
rs7330873	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7331814	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7339106	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7981788	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7991607	0.84[EUR][1000 genomes]
rs7997035	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7997333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7998025	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9301979	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9301981	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9301983	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9516437	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9516438	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9516440	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9516441	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9516443	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9516445	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516448	0.96[ASN][1000 genomes]
rs9524544	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524545	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524547	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9524548	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524549	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524550	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9524553	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9524554	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9524555	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524556	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524557	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524559	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524560	0.81[ASN][1000 genomes]
rs9524561	0.80[ASN][1000 genomes]
rs9524562	0.81[ASN][1000 genomes]
rs9524563	0.81[ASN][1000 genomes]
rs9524566	0.92[ASN][1000 genomes]
rs9524568	0.89[ASN][1000 genomes]
rs9556402	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9556405	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9561642	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9561643	0.92[ASN][1000 genomes]
rs9561645	0.96[ASN][1000 genomes]
rs9590037	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3897473	GPR180	cis	Nerve Tibial	GTEx
rs3897473	GPR180	cis	Artery Tibial	GTEx
rs3897473	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs3897473	GPR180	cis	lung	GTEx
rs3897473	GPR180	cis	Adipose Subcutaneous	GTEx
rs3897473	GPR180	cis	Muscle Skeletal	GTEx
rs3897473	GPR180	cis	Whole Blood	GTEx
rs3897473	GPR180	cis	Esophagus Mucosa	GTEx
rs3897473	GPR180	cis	Stomach	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95253000-95255600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:95253200-95254000	Enhancers	Placenta	Placenta
3	chr13:95253200-95254000	Weak transcription	HepG2	liver
4	chr13:95253200-95254600	Active TSS	Stomach Smooth Muscle	stomach
5	chr13:95253200-95254800	Active TSS	Brain Hippocampus Middle	brain
6	chr13:95253200-95255200	Active TSS	Brain Angular Gyrus	brain
7	chr13:95253200-95255800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:95253400-95254000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:95253400-95254200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:95253400-95254800	Active TSS	Colon Smooth Muscle	Colon
11	chr13:95253400-95254800	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr13:95253400-95255000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr13:95253400-95255000	Active TSS	Brain Substantia Nigra	brain
14	chr13:95253400-95255200	Active TSS	Fetal Kidney	kidney
15	chr13:95253600-95254000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr13:95253600-95254000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr13:95253600-95254000	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr13:95253600-95254000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr13:95253600-95254000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:95253600-95254000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr13:95253600-95254000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr13:95253600-95254000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:95253600-95254000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:95253600-95254000	Flanking Active TSS	Liver	Liver
25	chr13:95253600-95254000	Flanking Active TSS	Fetal Brain Male	brain
26	chr13:95253600-95254000	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr13:95253600-95254000	Flanking Active TSS	Fetal Thymus	thymus
28	chr13:95253600-95254000	Flanking Active TSS	Dnd41	blood
29	chr13:95253600-95254000	Flanking Active TSS	GM12878-XiMat	blood
30	chr13:95253600-95254000	Enhancers	K562	blood
31	chr13:95253600-95254200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr13:95253600-95254400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr13:95253600-95254600	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr13:95253600-95254600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr13:95253600-95254800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:95253600-95254800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:95253600-95254800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr13:95253600-95254800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr13:95253600-95254800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:95253600-95254800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:95253600-95254800	Active TSS	Brain Anterior Caudate	brain
42	chr13:95253600-95254800	Active TSS	Brain Cingulate Gyrus	brain
43	chr13:95253600-95254800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr13:95253600-95254800	Active TSS	Left Ventricle	heart
45	chr13:95253600-95254800	Active TSS	Lung	lung
46	chr13:95253600-95254800	Active TSS	Psoas Muscle	Psoas
47	chr13:95253600-95254800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr13:95253600-95254800	Active TSS	Stomach Mucosa	stomach
49	chr13:95253600-95254800	Active TSS	Hela-S3	cervix
50	chr13:95253600-95254800	Active TSS	NHLF	lung

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