Variant report

Variant	rs3763505
Chromosome Location	chr7:48128850-48128851
allele	C/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	REST	chr7:48128744-48129039	ECC-1	luminal epithelium:	n/a	chr7:48128890-48128903
4	EP300	chr7:48127907-48129373	ECC-1	luminal epithelium:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
5	SP4	chr7:48128733-48129292	H1-hESC	embryonic stem cell:	n/a	chr7:48129229-48129245
6	EBF1	chr7:48127988-48128947	GM12878	blood:	n/a	n/a
7	MXI1	chr7:48128166-48129638	H1-hESC	embryonic stem cell:	n/a	chr7:48129084-48129093 chr7:48128513-48128522 chr7:48128511-48128520
8	POLR2A	chr7:48127870-48130318	HUVEC	blood vessel:	n/a	n/a
9	NRF1	chr7:48127938-48129632	SK-N-SH	brain:	n/a	chr7:48128771-48128780 chr7:48129316-48129325
10	TCF12	chr7:48127818-48129161	SK-N-SH	brain:	n/a	chr7:48128593-48128603
11	E2F6	chr7:48127898-48129193	A549	lung:	n/a	n/a
12	REST	chr7:48127861-48129117	PANC-1	pancreas:	n/a	chr7:48128890-48128903
13	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
14	YY1	chr7:48127872-48129202	HepG2	liver:	n/a	chr7:48127933-48127942 chr7:48128889-48128903
15	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
16	HMGN3	chr7:48127954-48129487	K562	blood:	n/a	chr7:48129474-48129481
17	RELA	chr7:48127979-48129211	GM12891	blood:	n/a	n/a
18	BRCA1	chr7:48127936-48128950	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:48128093-48129062	HepG2	liver:	n/a	n/a
20	BCL3	chr7:48127832-48128963	A549	lung:	n/a	chr7:48128399-48128412 chr7:48128192-48128201 chr7:48127986-48127999 chr7:48128494-48128503 chr7:48128399-48128412
21	PAX5	chr7:48128591-48128991	GM12892	blood:	n/a	n/a
22	CEBPD	chr7:48128339-48128965	HepG2	liver:	n/a	n/a
23	CEBPB	chr7:48127757-48129284	Hela-S3	cervix:	n/a	n/a
24	TAF1	chr7:48128715-48129033	PFSK-1	brain:	n/a	n/a
25	REST	chr7:48128758-48129158	A549	lung:	n/a	chr7:48128890-48128903
26	CHD2	chr7:48127896-48129572	Hela-S3	cervix:	n/a	chr7:48129431-48129441 chr7:48129033-48129043
27	POLR2A	chr7:48127905-48128898	HL-60	blood:	n/a	n/a
28	RCOR1	chr7:48127787-48129377	K562	blood:	n/a	n/a
29	YY1	chr7:48128721-48129072	GM12891	blood:	n/a	chr7:48128889-48128903
30	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
31	POLR2A	chr7:48127924-48128904	K562	blood:	n/a	n/a
32	ATF2	chr7:48128684-48129119	H1-hESC	embryonic stem cell:	n/a	n/a
33	USF2	chr7:48127998-48129280	H1-hESC	embryonic stem cell:	n/a	chr7:48128098-48128114 chr7:48128510-48128521
34	TBP	chr7:48128051-48129011	K562	blood:	n/a	n/a
35	POLR2A	chr7:48127651-48129405	HepG2	liver:	n/a	n/a
36	USF1	chr7:48128015-48129229	SK-N-SH_RA	brain:	n/a	chr7:48128098-48128114 chr7:48129081-48129092 chr7:48128510-48128521
37	POLR2A	chr7:48127913-48128996	K562	blood:	n/a	n/a
38	TBP	chr7:48127924-48128996	Hela-S3	cervix:	n/a	n/a
39	ZNF143	chr7:48127938-48129219	H1-hESC	embryonic stem cell:	n/a	n/a
40	TBL1XR1	chr7:48128067-48129150	K562	blood:	n/a	n/a
41	EP300	chr7:48128025-48128863	SK-N-SH_RA	brain:	n/a	chr7:48128395-48128411 chr7:48128392-48128408 chr7:48128192-48128201 chr7:48128100-48128116
42	RELA	chr7:48128043-48129021	GM19099	blood:	n/a	n/a
43	REST	chr7:48128355-48129201	PFSK-1	brain:	n/a	chr7:48128890-48128903
44	CHD2	chr7:48128070-48129229	HepG2	liver:	n/a	chr7:48129033-48129043
45	JUND	chr7:48127969-48129135	Hela-S3	cervix:	n/a	chr7:48128191-48128202 chr7:48128192-48128202 chr7:48128193-48128202 chr7:48128192-48128202 chr7:48128192-48128202 chr7:48128192-48128202
46	YY1	chr7:48128446-48129170	SK-N-SH_RA	brain:	n/a	chr7:48128889-48128903
47	RXRA	chr7:48127814-48129161	SK-N-SH	brain:	n/a	chr7:48128192-48128201 chr7:48128133-48128146 chr7:48128133-48128146 chr7:48128133-48128146 chr7:48128453-48128462 chr7:48128132-48128146
48	MAFK	chr7:48127912-48128966	Hela-S3	cervix:	n/a	n/a
49	REST	chr7:48127826-48129231	A549	lung:	n/a	chr7:48128890-48128903
50	POLR2A	chr7:48128747-48129004	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:48128821-48128871	GM12878	blood:	n/a
2	chr7:48128821-48128871	PFSK-1	brain:	n/a
3	chr7:48128821-48128871	HCPEpiC	choroid plexus:	n/a
4	chr7:48128821-48128871	HUVEC	blood vessel:	n/a
5	chr7:48128821-48128871	HMEC	breast:	n/a
6	chr7:48128821-48128871	Hela-S3	cervix:	n/a
7	chr7:48128821-48128871	HRE	kidney:	n/a
8	chr7:48128821-48128871	HIPEpiC	eye:	n/a
9	chr7:48128821-48128871	Jurkat	blood:	n/a
10	chr7:48128821-48128871	NT2-D1	testis:	n/a
11	chr7:48128821-48128871	GM12891	blood:	n/a
12	chr7:48128821-48128871	HCF	heart:	n/a
13	chr7:48128821-48128871	HRPEpiC	eye:	n/a
14	chr7:48128821-48128871	HAEpiC	amniotic membrane:	n/a
15	chr7:48128821-48128871	HPAEpiC	pulmonary alveolar:	n/a
16	chr7:48128821-48128871	PANC-1	pancreas:	n/a
17	chr7:48128821-48128871	NHBE	bronchial:	n/a
18	chr7:48128821-48128871	AG04450	lung:	fetal
19	chr7:48128821-48128871	K562	blood:	n/a
20	chr7:48128821-48128871	LNCaP	prostate:	n/a
21	chr7:48128821-48128871	CMK	blood:	n/a
22	chr7:48128821-48128871	SKMC	muscle:	n/a
23	chr7:48128821-48128871	MCF10A-Er-Src	breast:	n/a
24	chr7:48128821-48128871	ProgFib	skin:	n/a
25	chr7:48128821-48128871	HL-60	blood:	n/a
26	chr7:48128821-48128871	HCM	heart:	n/a
27	chr7:48128821-48128871	ovcar-3	ovarian:	n/a
28	chr7:48128821-48128871	Hepatocyte	liver:	n/a
29	chr7:48128821-48128871	HepG2	liver:	n/a
30	chr7:48128821-48128871	HNPCEpiC	eye:	n/a
31	chr7:48128821-48128871	BJ	skin:	n/a
32	chr7:48128821-48128871	HEEpiC	esophagus:	n/a
33	chr7:48128821-48128871	AG09309	skin:	n/a
34	chr7:48128821-48128871	A549	lung:	n/a
35	chr7:48128821-48128871	H1-hESC	embryonic stem cell:	embryo
36	chr7:48128821-48128871	NB4	blood:	n/a
37	chr7:48128821-48128871	IMR90	lung:	fetal
38	chr7:48128821-48128871	SAEC	small airway:	n/a
39	chr7:48128821-48128871	AoSMC	blood vessel:	n/a
40	chr7:48128821-48128871	GM06990	blood:	n/a
41	chr7:48128821-48128871	ECC-1	luminal epithelium:	n/a
42	chr7:48128821-48128871	BE2_C	brain:	n/a
43	chr7:48128821-48128871	RPTEC	kidney:	n/a
44	chr7:48128821-48128871	U87	brain:	n/a
45	chr7:48128821-48128871	GM12892	blood:	n/a
46	chr7:48128821-48128871	NHDF-neo	bronchial:	n/a
47	chr7:48128821-48128871	HEK293	kidney:	embryo
48	chr7:48128821-48128871	T-47D	breast:	n/a
49	chr7:48128821-48128871	PrEC	prostate:	n/a
50	chr7:48128821-48128871	AG10803	skin:	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:
6	chr2:190648263..190649127-chr7:48128850..48129707,2	Hela-S3	cervix:
7	chr5:130970796..130971763-chr7:48128717..48129217,2	Hela-S3	cervix:

Variant related genes	Relation type
UPP1	TF binding region
UPP1	CpG island
ENSG00000224418	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000136273	Chromatin interaction
ENSG00000158987	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10278152	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11768083	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13227958	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13240650	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554494	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1581415	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1581416	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2686796	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2686800	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2686802	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2686803	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2708866	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2708867	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2708868	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2708869	0.88[EUR][1000 genomes]
rs2708870	0.88[EUR][1000 genomes]
rs2708871	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3752889	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3752890	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3763504	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59688958	0.82[AMR][1000 genomes]
rs62447120	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6968763	0.88[EUR][1000 genomes]
rs7341420	0.80[AMR][1000 genomes]
rs7385009	0.80[AMR][1000 genomes]
rs7458962	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7459020	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7793905	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7794100	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7804178	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639019	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9639991	0.86[AMR][1000 genomes];0.90[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
rs3763505	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	chr7:48128000-48129000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:48128000-48129200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:48128000-48129200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr7:48128000-48129200	Active TSS	Pancreas	Pancrea
29	chr7:48128000-48129400	Bivalent/Poised TSS	Fetal Brain Female	brain
30	chr7:48128000-48129400	Active TSS	Spleen	Spleen
31	chr7:48128000-48129600	Active TSS	Aorta	Aorta
32	chr7:48128000-48129600	Active TSS	Brain Angular Gyrus	brain
33	chr7:48128000-48129600	Active TSS	Duodenum Mucosa	Duodenum
34	chr7:48128000-48129600	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr7:48128000-48129800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:48128000-48129800	Active TSS	Lung	lung
38	chr7:48128000-48130000	Active TSS	Left Ventricle	heart
39	chr7:48128000-48130000	Active TSS	A549	lung
40	chr7:48128000-48130000	Active TSS	HSMMtube	muscle
41	chr7:48128000-48130200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr7:48128000-48130200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:48128000-48130200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:48128000-48130200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr7:48128000-48130200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:48128000-48130400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:48128000-48130600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:48128000-48131200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr7:48128200-48129000	Active TSS	Colonic Mucosa	Colon
50	chr7:48128200-48129400	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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