Variant report

Variant	rs10278152
Chromosome Location	chr7:48128657-48128658
allele	A/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	PAX5	chr7:48127837-48129002	GM12878	blood:	n/a	n/a
2	PBX3	chr7:48127957-48129077	A549	lung:	n/a	n/a
3	POLR2A	chr7:48128562-48128674	A549	lung:	n/a	n/a
4	USF1	chr7:48128291-48128662	K562	blood:	n/a	chr7:48128510-48128521
5	TEAD4	chr7:48127929-48128710	A549	lung:	n/a	n/a
6	EP300	chr7:48128022-48128684	GM12878	blood:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
7	EP300	chr7:48127907-48129373	ECC-1	luminal epithelium:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
8	EBF1	chr7:48127988-48128947	GM12878	blood:	n/a	n/a
9	FOXA1	chr7:48127898-48128787	HepG2	liver:	n/a	n/a
10	MXI1	chr7:48128166-48129638	H1-hESC	embryonic stem cell:	n/a	chr7:48129084-48129093 chr7:48128513-48128522 chr7:48128511-48128520
11	POLR2A	chr7:48127870-48130318	HUVEC	blood vessel:	n/a	n/a
12	NRF1	chr7:48127938-48129632	SK-N-SH	brain:	n/a	chr7:48128771-48128780 chr7:48129316-48129325
13	TCF12	chr7:48127818-48129161	SK-N-SH	brain:	n/a	chr7:48128593-48128603
14	E2F6	chr7:48127898-48129193	A549	lung:	n/a	n/a
15	REST	chr7:48127861-48129117	PANC-1	pancreas:	n/a	chr7:48128890-48128903
16	STAT3	chr7:48127929-48128830	MCF10A-Er-Src	breast:	n/a	chr7:48128193-48128202 chr7:48128438-48128446 chr7:48128803-48128815
17	ELF1	chr7:48127915-48128797	K562	blood:	n/a	n/a
18	MAX	chr7:48127995-48129429	H1-hESC	embryonic stem cell:	n/a	chr7:48128512-48128521 chr7:48128510-48128523 chr7:48129082-48129093 chr7:48128508-48128523 chr7:48128511-48128522 chr7:48129083-48129093 chr7:48128511-48128520 chr7:48129082-48129093 chr7:48129083-48129092 chr7:48128510-48128525 chr7:48129237-48129246 chr7:48128192-48128201 chr7:48128512-48128522 chr7:48128511-48128521 chr7:48129081-48129094 chr7:48128512-48128522 chr7:48129082-48129092 chr7:48129084-48129091 chr7:48129083-48129092 chr7:48128511-48128522
19	YY1	chr7:48127872-48129202	HepG2	liver:	n/a	chr7:48127933-48127942 chr7:48128889-48128903
20	TFAP2A	chr7:48127902-48129241	Hela-S3	cervix:	n/a	chr7:48128798-48128806 chr7:48128798-48128806 chr7:48128099-48128114 chr7:48129022-48129034 chr7:48128798-48128806 chr7:48128797-48128812
21	REST	chr7:48128004-48128689	HepG2	liver:	n/a	n/a
22	CEBPB	chr7:48128306-48128840	MCF-7	breast:	n/a	n/a
23	HMGN3	chr7:48127954-48129487	K562	blood:	n/a	chr7:48129474-48129481
24	USF1	chr7:48127921-48128786	A549	lung:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
25	RELA	chr7:48127979-48129211	GM12891	blood:	n/a	n/a
26	BRCA1	chr7:48127936-48128950	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr7:48128093-48129062	HepG2	liver:	n/a	n/a
28	BCL3	chr7:48127832-48128963	A549	lung:	n/a	chr7:48128399-48128412 chr7:48128192-48128201 chr7:48127986-48127999 chr7:48128494-48128503 chr7:48128399-48128412
29	FOSL2	chr7:48127894-48128686	HepG2	liver:	n/a	chr7:48128192-48128202 chr7:48128193-48128202 chr7:48128190-48128201 chr7:48128192-48128202 chr7:48128192-48128202 chr7:48128192-48128202
30	PAX5	chr7:48128591-48128991	GM12892	blood:	n/a	n/a
31	USF2	chr7:48127965-48128715	Hela-S3	cervix:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
32	CEBPD	chr7:48128339-48128965	HepG2	liver:	n/a	n/a
33	CEBPB	chr7:48127757-48129284	Hela-S3	cervix:	n/a	n/a
34	CHD2	chr7:48127896-48129572	Hela-S3	cervix:	n/a	chr7:48129431-48129441 chr7:48129033-48129043
35	POLR2A	chr7:48127905-48128898	HL-60	blood:	n/a	n/a
36	FOXA1	chr7:48128007-48128835	HepG2	liver:	n/a	n/a
37	RCOR1	chr7:48127787-48129377	K562	blood:	n/a	n/a
38	HEY1	chr7:48127905-48128679	K562	blood:	n/a	chr7:48128398-48128413
39	MAX	chr7:48128027-48129186	A549	lung:	n/a	chr7:48128512-48128521 chr7:48128510-48128523 chr7:48129082-48129093 chr7:48128508-48128523 chr7:48128511-48128522 chr7:48129083-48129093 chr7:48128511-48128520 chr7:48129082-48129093 chr7:48129083-48129092 chr7:48128510-48128525 chr7:48128192-48128201 chr7:48128512-48128522 chr7:48128511-48128521 chr7:48129081-48129094 chr7:48128512-48128522 chr7:48129082-48129092 chr7:48129084-48129091 chr7:48129083-48129092 chr7:48128511-48128522
40	EBF1	chr7:48128030-48128767	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:48127924-48128904	K562	blood:	n/a	n/a
42	USF2	chr7:48127998-48129280	H1-hESC	embryonic stem cell:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
43	TBP	chr7:48128051-48129011	K562	blood:	n/a	n/a
44	POLR2A	chr7:48127651-48129405	HepG2	liver:	n/a	n/a
45	USF1	chr7:48128015-48129229	SK-N-SH_RA	brain:	n/a	chr7:48128098-48128114 chr7:48129081-48129092 chr7:48128510-48128521
46	POLR2A	chr7:48127913-48128996	K562	blood:	n/a	n/a
47	SIN3AK20	chr7:48128408-48128657	SK-N-SH	brain:	n/a	n/a
48	TBP	chr7:48127924-48128996	Hela-S3	cervix:	n/a	n/a
49	ZNF143	chr7:48127938-48129219	H1-hESC	embryonic stem cell:	n/a	n/a
50	TBL1XR1	chr7:48128067-48129150	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:48128611-48128661	MCF10A-Er-Src	breast:	n/a
2	chr7:48128611-48128661	A549	lung:	n/a
3	chr7:48128611-48128661	H1-hESC	embryonic stem cell:	embryo
4	chr7:48128611-48128661	GM06990	blood:	n/a
5	chr7:48128624-48128674	SK-N-MC	brain:	n/a
6	chr7:48128624-48128674	SAEC	small airway:	n/a
7	chr7:48128611-48128661	HMEC	breast:	n/a
8	chr7:48128624-48128674	ProgFib	skin:	n/a
9	chr7:48128624-48128674	Caco-2	colon:	n/a
10	chr7:48128611-48128661	NH-A	brain:	n/a
11	chr7:48128611-48128661	HRPEpiC	eye:	n/a
12	chr7:48128611-48128661	Caco-2	colon:	n/a
13	chr7:48128611-48128661	SKMC	muscle:	n/a
14	chr7:48128611-48128661	SAEC	small airway:	n/a
15	chr7:48128624-48128674	GM06990	blood:	n/a
16	chr7:48128624-48128674	T-47D	breast:	n/a
17	chr7:48128611-48128661	ovcar-3	ovarian:	n/a
18	chr7:48128624-48128674	HCM	heart:	n/a
19	chr7:48128624-48128674	ovcar-3	ovarian:	n/a
20	chr7:48128624-48128674	LNCaP	prostate:	n/a
21	chr7:48128611-48128661	NHBE	bronchial:	n/a
22	chr7:48128611-48128661	HEEpiC	esophagus:	n/a
23	chr7:48128611-48128661	MCF-7	breast:	n/a
24	chr7:48128624-48128674	PrEC	prostate:	n/a
25	chr7:48128624-48128674	HAEpiC	amniotic membrane:	n/a
26	chr7:48128611-48128661	ECC-1	luminal epithelium:	n/a
27	chr7:48128624-48128674	AG09309	skin:	n/a
28	chr7:48128624-48128674	NB4	blood:	n/a
29	chr7:48128624-48128674	MCF10A-Er-Src	breast:	n/a
30	chr7:48128624-48128674	SK-N-SH_RA	brain:	n/a
31	chr7:48128624-48128674	HRE	kidney:	n/a
32	chr7:48128611-48128661	GM19239	blood:	n/a
33	chr7:48128624-48128674	U87	brain:	n/a
34	chr7:48128624-48128674	HCPEpiC	choroid plexus:	n/a
35	chr7:48128624-48128674	HepG2	liver:	n/a
36	chr7:48128624-48128674	HUVEC	blood vessel:	n/a
37	chr7:48128611-48128661	T-47D	breast:	n/a
38	chr7:48128611-48128661	HCT-116	colon:	n/a
39	chr7:48128624-48128674	PFSK-1	brain:	n/a
40	chr7:48128611-48128661	HPAEpiC	pulmonary alveolar:	n/a
41	chr7:48128611-48128661	RPTEC	kidney:	n/a
42	chr7:48128611-48128661	ProgFib	skin:	n/a
43	chr7:48128611-48128661	HRE	kidney:	n/a
44	chr7:48128611-48128661	HCF	heart:	n/a
45	chr7:48128611-48128661	SK-N-SH	brain:	n/a
46	chr7:48128611-48128661	HL-60	blood:	n/a
47	chr7:48128611-48128661	GM12878	blood:	n/a
48	chr7:48128624-48128674	PANC-1	pancreas:	n/a
49	chr7:48128624-48128674	IMR90	lung:	fetal
50	chr7:48128624-48128674	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74230393..74231038-chr7:48128462..48129209,2	HCT-116	colon:
2	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:
3	chr13:99229380..99229995-chr7:48128637..48129292,2	Hela-S3	cervix:
4	chr7:48017568..48020341-chr7:48128356..48131105,2	MCF-7	breast:
5	chr7:48017535..48019169-chr7:48128413..48129998,2	K562	blood:

Variant related genes	Relation type
UPP1	TF binding region
UPP1	CpG island
ENSG00000136273	Chromatin interaction
ENSG00000224418	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11768083	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240650	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554494	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581415	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581416	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686796	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686800	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686802	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686803	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708866	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708867	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708868	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708869	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708870	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708871	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3752889	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752890	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763505	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62447120	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968763	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7458962	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459020	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793905	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794100	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804178	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639019	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639991	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription 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	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv997355	chr7:48128431-48138826	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10278152	UPP1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48127200-48129600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:48127200-48129600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr7:48127600-48129600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:48127600-48129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:48127600-48130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:48127600-48130200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr7:48127600-48130200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr7:48127600-48130200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr7:48127600-48130400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:48127600-48130400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr7:48127600-48130400	Active TSS	Rectal Smooth Muscle	rectum
12	chr7:48127600-48130600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr7:48127800-48129000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:48127800-48129400	Active TSS	HepG2	liver
15	chr7:48127800-48129600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:48127800-48129800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:48127800-48129800	Active TSS	Brain Anterior Caudate	brain
18	chr7:48127800-48130200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:48127800-48130200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:48127800-48130200	Active TSS	Colon Smooth Muscle	Colon
21	chr7:48127800-48130200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr7:48127800-48130400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr7:48127800-48130400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr7:48127800-48130600	Active TSS	Psoas Muscle	Psoas
25	chr7:48128000-48128800	Bivalent Enhancer	Fetal Brain Male	brain
26	chr7:48128000-48129000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:48128000-48129200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr7:48128000-48129200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr7:48128000-48129200	Active TSS	Pancreas	Pancrea
30	chr7:48128000-48129400	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr7:48128000-48129400	Active TSS	Spleen	Spleen
32	chr7:48128000-48129600	Active TSS	Aorta	Aorta
33	chr7:48128000-48129600	Active TSS	Brain Angular Gyrus	brain
34	chr7:48128000-48129600	Active TSS	Duodenum Mucosa	Duodenum
35	chr7:48128000-48129600	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:48128000-48129800	Active TSS	Lung	lung
39	chr7:48128000-48130000	Active TSS	Left Ventricle	heart
40	chr7:48128000-48130000	Active TSS	A549	lung
41	chr7:48128000-48130000	Active TSS	HSMMtube	muscle
42	chr7:48128000-48130200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr7:48128000-48130200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:48128000-48130200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:48128000-48130200	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr7:48128000-48130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:48128000-48130400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:48128000-48130600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:48128000-48131200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr7:48128200-48128800	Active TSS	Brain Germinal Matrix	brain

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