Variant report

Variant	rs7458962
Chromosome Location	chr7:48128558-48128559
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	USF1	chr7:48128291-48128662	K562	blood:	n/a	chr7:48128510-48128521
4	TEAD4	chr7:48127929-48128710	A549	lung:	n/a	n/a
5	EP300	chr7:48128022-48128684	GM12878	blood:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
6	EP300	chr7:48127907-48129373	ECC-1	luminal epithelium:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
7	EBF1	chr7:48127988-48128947	GM12878	blood:	n/a	n/a
8	FOXA1	chr7:48127898-48128787	HepG2	liver:	n/a	n/a
9	MXI1	chr7:48128166-48129638	H1-hESC	embryonic stem cell:	n/a	chr7:48129084-48129093 chr7:48128513-48128522 chr7:48128511-48128520
10	MBD4	chr7:48128300-48128592	HepG2	liver:	n/a	n/a
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	GATA2	chr7:48127989-48128595	HUVEC	blood vessel:	n/a	chr7:48128191-48128200
19	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
20	YY1	chr7:48127872-48129202	HepG2	liver:	n/a	chr7:48127933-48127942 chr7:48128889-48128903
21	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
22	REST	chr7:48128004-48128689	HepG2	liver:	n/a	n/a
23	CEBPB	chr7:48128306-48128840	MCF-7	breast:	n/a	n/a
24	HMGN3	chr7:48127954-48129487	K562	blood:	n/a	chr7:48129474-48129481
25	USF1	chr7:48127921-48128786	A549	lung:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
26	RELA	chr7:48127979-48129211	GM12891	blood:	n/a	n/a
27	BRCA1	chr7:48127936-48128950	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr7:48128271-48128559	GM12891	blood:	n/a	n/a
29	POLR2A	chr7:48128093-48129062	HepG2	liver:	n/a	n/a
30	BCL3	chr7:48127832-48128963	A549	lung:	n/a	chr7:48128399-48128412 chr7:48128192-48128201 chr7:48127986-48127999 chr7:48128494-48128503 chr7:48128399-48128412
31	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
32	NFIC	chr7:48128115-48128643	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr7:48128175-48128584	H1-hESC	embryonic stem cell:	n/a	n/a
34	USF2	chr7:48127965-48128715	Hela-S3	cervix:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
35	CEBPD	chr7:48128339-48128965	HepG2	liver:	n/a	n/a
36	CEBPB	chr7:48127757-48129284	Hela-S3	cervix:	n/a	n/a
37	CHD2	chr7:48127896-48129572	Hela-S3	cervix:	n/a	chr7:48129431-48129441 chr7:48129033-48129043
38	POLR2A	chr7:48127905-48128898	HL-60	blood:	n/a	n/a
39	FOXA1	chr7:48128007-48128835	HepG2	liver:	n/a	n/a
40	RCOR1	chr7:48127787-48129377	K562	blood:	n/a	n/a
41	HEY1	chr7:48127905-48128679	K562	blood:	n/a	chr7:48128398-48128413
42	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
43	EBF1	chr7:48128030-48128767	GM12878	blood:	n/a	n/a
44	POLR2A	chr7:48127924-48128904	K562	blood:	n/a	n/a
45	USF2	chr7:48127998-48129280	H1-hESC	embryonic stem cell:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
46	TBP	chr7:48128051-48129011	K562	blood:	n/a	n/a
47	POLR2A	chr7:48127651-48129405	HepG2	liver:	n/a	n/a
48	USF1	chr7:48128015-48129229	SK-N-SH_RA	brain:	n/a	chr7:48128098-48128114 chr7:48129081-48129092 chr7:48128510-48128521
49	POLR2A	chr7:48127913-48128996	K562	blood:	n/a	n/a
50	SIN3AK20	chr7:48128408-48128657	SK-N-SH	brain:	n/a	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	chr7:26903972..26904735-chr7:48127989..48128616,2	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
ENSG00000156508	Chromatin interaction
ENSG00000136273	Chromatin interaction
ENSG00000005020	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10278152	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768083	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240650	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554494	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581415	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581416	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686796	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686800	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686802	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686803	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708866	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708867	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708868	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708869	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708870	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708871	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3752889	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752890	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763505	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.83[ASN][1000 genomes]
rs62447120	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968763	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7459020	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793905	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794100	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804178	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639019	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639991	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7458962	UPP1	cis	Muscle Skeletal	GTEx
rs7458962	UPP1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48126200-48128600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr7:48127200-48129600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:48127200-48129600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr7:48127600-48128600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:48127600-48129600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:48127600-48129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr7:48127600-48130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:48127600-48130200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr7:48127600-48130200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:48127600-48130200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr7:48127600-48130400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:48127600-48130400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr7:48127600-48130400	Active TSS	Rectal Smooth Muscle	rectum
14	chr7:48127600-48130600	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr7:48127800-48128600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:48127800-48128600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr7:48127800-48128600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr7:48127800-48128600	Flanking Active TSS	HSMM	muscle
19	chr7:48127800-48128600	Flanking Active TSS	HUVEC	blood vessel
20	chr7:48127800-48129000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:48127800-48129400	Active TSS	HepG2	liver
22	chr7:48127800-48129600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:48127800-48129800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr7:48127800-48129800	Active TSS	Brain Anterior Caudate	brain
25	chr7:48127800-48130200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr7:48127800-48130200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:48127800-48130200	Active TSS	Colon Smooth Muscle	Colon
28	chr7:48127800-48130200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr7:48127800-48130400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr7:48127800-48130400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr7:48127800-48130600	Active TSS	Psoas Muscle	Psoas
32	chr7:48128000-48128600	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr7:48128000-48128600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr7:48128000-48128600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr7:48128000-48128600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr7:48128000-48128600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr7:48128000-48128600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr7:48128000-48128600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:48128000-48128600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr7:48128000-48128600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:48128000-48128600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:48128000-48128600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr7:48128000-48128600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr7:48128000-48128600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr7:48128000-48128600	Flanking Active TSS	HMEC	breast
46	chr7:48128000-48128600	Flanking Active TSS	NH-A	brain
47	chr7:48128000-48128800	Bivalent Enhancer	Fetal Brain Male	brain
48	chr7:48128000-48129000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:48128000-48129200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr7:48128000-48129200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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