Variant report

Variant	rs1554494
Chromosome Location	chr7:48128189-48128190
allele	A/G
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	GABPA	chr7:48128017-48128326	Hela-S3	cervix:	n/a	n/a
2	PAX5	chr7:48127837-48129002	GM12878	blood:	n/a	n/a
3	PBX3	chr7:48127957-48129077	A549	lung:	n/a	n/a
4	JUN	chr7:48128069-48128314	HepG2	liver:	n/a	chr7:48128192-48128202 chr7:48128193-48128202 chr7:48128192-48128202 chr7:48128192-48128202 chr7:48128192-48128202
5	FOSL2	chr7:48127936-48128480	MCF-7	breast:	n/a	chr7:48128192-48128202 chr7:48128193-48128202 chr7:48128190-48128201 chr7:48128192-48128202 chr7:48128192-48128202 chr7:48128192-48128202
6	TEAD4	chr7:48127929-48128710	A549	lung:	n/a	n/a
7	CTCF	chr7:48128140-48128290	GM12873	blood:	n/a	n/a
8	EP300	chr7:48127982-48128430	SK-N-SH_RA	brain:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
9	EP300	chr7:48128022-48128684	GM12878	blood:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
10	EP300	chr7:48127907-48129373	ECC-1	luminal epithelium:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
11	JUND	chr7:48128055-48128296	HepG2	liver:	n/a	chr7:48128191-48128202 chr7:48128192-48128202 chr7:48128193-48128202 chr7:48128192-48128202 chr7:48128192-48128202 chr7:48128192-48128202
12	EBF1	chr7:48127988-48128947	GM12878	blood:	n/a	n/a
13	FOXA1	chr7:48127898-48128787	HepG2	liver:	n/a	n/a
14	MXI1	chr7:48128166-48129638	H1-hESC	embryonic stem cell:	n/a	chr7:48129084-48129093 chr7:48128513-48128522 chr7:48128511-48128520
15	POLR2A	chr7:48127870-48130318	HUVEC	blood vessel:	n/a	n/a
16	NRF1	chr7:48127938-48129632	SK-N-SH	brain:	n/a	chr7:48128771-48128780 chr7:48129316-48129325
17	REST	chr7:48127971-48128446	K562	blood:	n/a	n/a
18	TCF12	chr7:48127818-48129161	SK-N-SH	brain:	n/a	chr7:48128593-48128603
19	E2F6	chr7:48127898-48129193	A549	lung:	n/a	n/a
20	REST	chr7:48127861-48129117	PANC-1	pancreas:	n/a	chr7:48128890-48128903
21	STAT3	chr7:48127929-48128830	MCF10A-Er-Src	breast:	n/a	chr7:48128193-48128202 chr7:48128438-48128446 chr7:48128803-48128815
22	ELF1	chr7:48127915-48128797	K562	blood:	n/a	n/a
23	GATA2	chr7:48127989-48128595	HUVEC	blood vessel:	n/a	chr7:48128191-48128200
24	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
25	YY1	chr7:48127872-48129202	HepG2	liver:	n/a	chr7:48127933-48127942 chr7:48128889-48128903
26	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
27	REST	chr7:48128004-48128689	HepG2	liver:	n/a	n/a
28	HMGN3	chr7:48127954-48129487	K562	blood:	n/a	chr7:48129474-48129481
29	USF1	chr7:48127921-48128786	A549	lung:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
30	RELA	chr7:48127979-48129211	GM12891	blood:	n/a	n/a
31	BRCA1	chr7:48127936-48128950	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr7:48128093-48129062	HepG2	liver:	n/a	n/a
33	BCL3	chr7:48127832-48128963	A549	lung:	n/a	chr7:48128399-48128412 chr7:48128192-48128201 chr7:48127986-48127999 chr7:48128494-48128503 chr7:48128399-48128412
34	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
35	NFIC	chr7:48128115-48128643	GM12878	blood:	n/a	n/a
36	ZBTB7A	chr7:48127931-48128360	ECC-1	luminal epithelium:	n/a	chr7:48128349-48128360
37	SIN3AK20	chr7:48128175-48128584	H1-hESC	embryonic stem cell:	n/a	n/a
38	USF2	chr7:48127965-48128715	Hela-S3	cervix:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
39	CEBPB	chr7:48127757-48129284	Hela-S3	cervix:	n/a	n/a
40	CHD2	chr7:48127896-48129572	Hela-S3	cervix:	n/a	chr7:48129431-48129441 chr7:48129033-48129043
41	POLR2A	chr7:48127905-48128898	HL-60	blood:	n/a	n/a
42	FOXA1	chr7:48128007-48128835	HepG2	liver:	n/a	n/a
43	RCOR1	chr7:48127787-48129377	K562	blood:	n/a	n/a
44	HEY1	chr7:48127905-48128679	K562	blood:	n/a	chr7:48128398-48128413
45	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
46	YY1	chr7:48127979-48128345	HCT-116	colon:	n/a	n/a
47	CTCF	chr7:48128022-48128223	GM12878	blood:	n/a	chr7:48128127-48128136 chr7:48128103-48128116 chr7:48128123-48128136
48	EBF1	chr7:48128030-48128767	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:48127924-48128904	K562	blood:	n/a	n/a
50	USF2	chr7:48127998-48129280	H1-hESC	embryonic stem cell:	n/a	chr7:48128098-48128114 chr7:48128510-48128521

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:48128151-48128201	PFSK-1	brain:	n/a
2	chr7:48128151-48128201	MCF10A-Er-Src	breast:	n/a
3	chr7:48128151-48128201	HAEpiC	amniotic membrane:	n/a
4	chr7:48128151-48128201	HCF	heart:	n/a
5	chr7:48128151-48128201	AG09309	skin:	n/a
6	chr7:48128151-48128201	ovcar-3	ovarian:	n/a
7	chr7:48128151-48128201	NT2-D1	testis:	n/a
8	chr7:48128151-48128201	SK-N-SH_RA	brain:	n/a
9	chr7:48128151-48128201	ProgFib	skin:	n/a
10	chr7:48128151-48128201	HRE	kidney:	n/a
11	chr7:48128151-48128201	MCF-7	breast:	n/a
12	chr7:48128151-48128201	NH-A	brain:	n/a
13	chr7:48128151-48128201	NB4	blood:	n/a
14	chr7:48128151-48128201	HCPEpiC	choroid plexus:	n/a
15	chr7:48128151-48128201	BE2_C	brain:	n/a
16	chr7:48128151-48128201	HL-60	blood:	n/a
17	chr7:48128151-48128201	AG04449	skin:	fetal
18	chr7:48128151-48128201	RPTEC	kidney:	n/a
19	chr7:48128151-48128201	GM19239	blood:	n/a
20	chr7:48128151-48128201	K562	blood:	n/a
21	chr7:48128151-48128201	HIPEpiC	eye:	n/a
22	chr7:48128151-48128201	T-47D	breast:	n/a
23	chr7:48128151-48128201	CMK	blood:	n/a
24	chr7:48128151-48128201	AG04450	lung:	fetal
25	chr7:48128151-48128201	IMR90	lung:	fetal
26	chr7:48128151-48128201	SAEC	small airway:	n/a
27	chr7:48128151-48128201	HMEC	breast:	n/a
28	chr7:48128151-48128201	Hepatocyte	liver:	n/a
29	chr7:48128151-48128201	GM12891	blood:	n/a
30	chr7:48128151-48128201	GM06990	blood:	n/a
31	chr7:48128151-48128201	PANC-1	pancreas:	n/a
32	chr7:48128151-48128201	Jurkat	blood:	n/a
33	chr7:48128151-48128201	HPAEpiC	pulmonary alveolar:	n/a
34	chr7:48128151-48128201	HepG2	liver:	n/a
35	chr7:48128151-48128201	ECC-1	luminal epithelium:	n/a
36	chr7:48128151-48128201	HCT-116	colon:	n/a
37	chr7:48128151-48128201	A549	lung:	n/a
38	chr7:48128151-48128201	U87	brain:	n/a
39	chr7:48128151-48128201	NHDF-neo	bronchial:	n/a
40	chr7:48128151-48128201	HRPEpiC	eye:	n/a
41	chr7:48128151-48128201	Hela-S3	cervix:	n/a
42	chr7:48128151-48128201	GM12878	blood:	n/a
43	chr7:48128151-48128201	HNPCEpiC	eye:	n/a
44	chr7:48128151-48128201	AG09319	gingival:	n/a
45	chr7:48128151-48128201	HEEpiC	esophagus:	n/a
46	chr7:48128151-48128201	HUVEC	blood vessel:	n/a
47	chr7:48128151-48128201	AoSMC	blood vessel:	n/a
48	chr7:48128151-48128201	NHBE	bronchial:	n/a
49	chr7:48128151-48128201	AG10803	skin:	n/a
50	chr7:48128151-48128201	SKMC	muscle:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:
2	chr7:26903972..26904735-chr7:48127989..48128616,2	Hela-S3	cervix:
3	chr7:48127890..48128535-chr7:114562417..114563199,2	Hela-S3	cervix:

Variant related genes	Relation type
UPP1	TF binding region
UPP1	CpG island
ENSG00000136273	Chromatin interaction
ENSG00000135272	Chromatin interaction
ENSG00000005020	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10278152	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768083	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13227958	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240650	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581415	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1581416	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686796	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2686800	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686802	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686803	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708866	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708867	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708868	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708869	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708870	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708871	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3752889	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763504	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763505	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.83[ASN][1000 genomes]
rs62447120	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968763	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7458962	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7459020	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7793905	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794100	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804178	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9639019	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639991	0.87[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1554494	UPP1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48122400-48128200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:48125400-48128200	Weak transcription	Fetal Heart	heart
3	chr7:48125800-48128200	Weak transcription	Gastric	stomach
4	chr7:48126200-48128600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr7:48127000-48128200	Enhancers	Primary B cells from cord blood	blood
6	chr7:48127200-48128400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr7:48127200-48129600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:48127200-48129600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr7:48127400-48128200	Weak transcription	Small Intestine	intestine
10	chr7:48127600-48128200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:48127600-48128200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:48127600-48128400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:48127600-48128400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:48127600-48128400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr7:48127600-48128400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr7:48127600-48128400	Flanking Active TSS	GM12878-XiMat	blood
17	chr7:48127600-48128400	Flanking Active TSS	NHEK	skin
18	chr7:48127600-48128600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:48127600-48129600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:48127600-48129600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr7:48127600-48130000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:48127600-48130200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr7:48127600-48130200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr7:48127600-48130200	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr7:48127600-48130400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:48127600-48130400	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr7:48127600-48130400	Active TSS	Rectal Smooth Muscle	rectum
28	chr7:48127600-48130600	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:48127800-48128200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:48127800-48128200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr7:48127800-48128200	Flanking Active TSS	Liver	Liver
32	chr7:48127800-48128200	Active TSS	Brain Cingulate Gyrus	brain
33	chr7:48127800-48128200	Flanking Active TSS	Esophagus	oesophagus
34	chr7:48127800-48128200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr7:48127800-48128200	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr7:48127800-48128200	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr7:48127800-48128200	Flanking Active TSS	Right Ventricle	heart
38	chr7:48127800-48128400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr7:48127800-48128400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr7:48127800-48128400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:48127800-48128400	Active TSS	Right Atrium	heart
42	chr7:48127800-48128400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr7:48127800-48128400	Flanking Active TSS	Osteobl	bone
44	chr7:48127800-48128600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:48127800-48128600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr7:48127800-48128600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr7:48127800-48128600	Flanking Active TSS	HSMM	muscle
48	chr7:48127800-48128600	Flanking Active TSS	HUVEC	blood vessel
49	chr7:48127800-48129000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:48127800-48129400	Active TSS	HepG2	liver

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