Variant report

Variant	rs116426957
Chromosome Location	chr3:47823549-47823550
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:533)
CpG islands
(count:122)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:533 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr3:47822633-47824066	Hela-S3	cervix:	n/a	chr3:47824011-47824018 chr3:47822976-47822986 chr3:47822973-47822987
2	POLR2A	chr3:47822481-47823987	HepG2	liver:	n/a	n/a
3	MAZ	chr3:47821979-47824044	GM12878	blood:	n/a	n/a
4	ZBTB33	chr3:47823025-47823766	SK-N-SH	brain:	n/a	n/a
5	NR2F2	chr3:47823313-47823886	K562	blood:	n/a	n/a
6	PML	chr3:47822488-47824564	GM12878	blood:	n/a	n/a
7	HEY1	chr3:47823014-47823738	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:47823156-47823671	A549	lung:	n/a	n/a
9	USF2	chr3:47823505-47823703	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:47822647-47824061	K562	blood:	n/a	n/a
11	TAF1	chr3:47823193-47823768	Hela-S3	cervix:	n/a	n/a
12	E2F4	chr3:47822763-47823926	K562	blood:	n/a	chr3:47823073-47823087 chr3:47823483-47823492 chr3:47823477-47823486
13	BATF	chr3:47823495-47823776	GM12878	blood:	n/a	n/a
14	MAX	chr3:47822488-47823923	SK-N-SH	brain:	n/a	n/a
15	RAD21	chr3:47823510-47823572	H1-hESC	embryonic stem cell:	n/a	n/a
16	MYC	chr3:47823434-47823704	Hela-S3	cervix:	n/a	n/a
17	YY1	chr3:47823017-47823735	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF384	chr3:47823200-47823750	K562	blood:	n/a	n/a
19	POLR2A	chr3:47821915-47824716	GM12878	blood:	n/a	n/a
20	YY1	chr3:47823057-47823779	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:47823124-47823841	A549	lung:	n/a	n/a
22	TCF3	chr3:47823404-47823629	GM12878	blood:	n/a	n/a
23	ELF1	chr3:47823162-47823726	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:47821719-47824693	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:47822343-47824121	GM12891	blood:	n/a	n/a
26	UBTF	chr3:47822787-47824076	K562	blood:	n/a	n/a
27	TAF1	chr3:47822655-47824105	K562	blood:	n/a	n/a
28	BCL3	chr3:47823281-47823798	A549	lung:	n/a	n/a
29	PAX5	chr3:47823157-47823961	GM12878	blood:	n/a	chr3:47823477-47823486
30	TAF7	chr3:47822612-47823796	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:47823096-47823810	HepG2	liver:	n/a	n/a
32	BACH1	chr3:47822846-47823713	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:47822396-47824476	HCT-116	colon:	n/a	n/a
34	CREB1	chr3:47822776-47823908	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr3:47822572-47823787	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr3:47823500-47823650	GM12873	blood:	n/a	n/a
37	GABPA	chr3:47823174-47823623	HepG2	liver:	n/a	chr3:47823482-47823493 chr3:47823473-47823487 chr3:47823476-47823487 chr3:47823482-47823491 chr3:47823482-47823496
38	FOXA2	chr3:47822769-47823575	A549	lung:	n/a	n/a
39	POLR2A	chr3:47822599-47823962	GM12878	blood:	n/a	n/a
40	GTF2F1	chr3:47823130-47823966	K562	blood:	n/a	n/a
41	POLR2A	chr3:47822617-47824614	GM18505	blood:	n/a	n/a
42	PAX5	chr3:47823478-47823791	GM12878	blood:	n/a	n/a
43	ARID3A	chr3:47823180-47823697	HepG2	liver:	n/a	n/a
44	TEAD4	chr3:47822150-47824143	K562	blood:	n/a	n/a
45	POLR2A	chr3:47822617-47824064	GM12878	blood:	n/a	n/a
46	BATF	chr3:47823375-47824031	GM12878	blood:	n/a	n/a
47	MYC	chr3:47822731-47823751	MCF-7	breast:	n/a	n/a
48	MYC	chr3:47822588-47823736	K562	blood:	n/a	n/a
49	PML	chr3:47823174-47823728	GM12878	blood:	n/a	n/a
50	MXI1	chr3:47821452-47824663	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:47823524-47823574	PFSK-1	brain:	n/a
2	chr3:47823524-47823574	GM12892	blood:	n/a
3	chr3:47823524-47823574	MCF-7	breast:	n/a
4	chr3:47823524-47823574	Caco-2	colon:	n/a
5	chr3:47823531-47823581	SKMC	muscle:	n/a
6	chr3:47823524-47823574	HIPEpiC	eye:	n/a
7	chr3:47823531-47823581	A549	lung:	n/a
8	chr3:47823524-47823574	SKMC	muscle:	n/a
9	chr3:47823524-47823574	A549	lung:	n/a
10	chr3:47823524-47823574	GM19239	blood:	n/a
11	chr3:47823524-47823574	SK-N-MC	brain:	n/a
12	chr3:47823524-47823574	H1-hESC	embryonic stem cell:	embryo
13	chr3:47823524-47823574	Hepatocyte	liver:	n/a
14	chr3:47823531-47823581	AG10803	skin:	n/a
15	chr3:47823531-47823581	SK-N-SH	brain:	n/a
16	chr3:47823531-47823581	NH-A	brain:	n/a
17	chr3:47823531-47823581	T-47D	breast:	n/a
18	chr3:47823524-47823574	HRPEpiC	eye:	n/a
19	chr3:47823531-47823581	HIPEpiC	eye:	n/a
20	chr3:47823524-47823574	HAEpiC	amniotic membrane:	n/a
21	chr3:47823524-47823574	BJ	skin:	n/a
22	chr3:47823531-47823581	H1-hESC	embryonic stem cell:	embryo
23	chr3:47823531-47823581	PANC-1	pancreas:	n/a
24	chr3:47823531-47823581	SK-N-MC	brain:	n/a
25	chr3:47823524-47823574	CMK	blood:	n/a
26	chr3:47823524-47823574	ovcar-3	ovarian:	n/a
27	chr3:47823524-47823574	AG09309	skin:	n/a
28	chr3:47823531-47823581	SAEC	small airway:	n/a
29	chr3:47823524-47823574	IMR90	lung:	fetal
30	chr3:47823531-47823581	HepG2	liver:	n/a
31	chr3:47823531-47823581	Caco-2	colon:	n/a
32	chr3:47823531-47823581	MCF10A-Er-Src	breast:	n/a
33	chr3:47823524-47823574	PANC-1	pancreas:	n/a
34	chr3:47823531-47823581	IMR90	lung:	fetal
35	chr3:47823524-47823574	BE2_C	brain:	n/a
36	chr3:47823524-47823574	HCPEpiC	choroid plexus:	n/a
37	chr3:47823531-47823581	MCF-7	breast:	n/a
38	chr3:47823531-47823581	LNCaP	prostate:	n/a
39	chr3:47823531-47823581	HRE	kidney:	n/a
40	chr3:47823524-47823574	GM06990	blood:	n/a
41	chr3:47823524-47823574	HUVEC	blood vessel:	n/a
42	chr3:47823531-47823581	Hela-S3	cervix:	n/a
43	chr3:47823531-47823581	AG04450	lung:	fetal
44	chr3:47823524-47823574	HEEpiC	esophagus:	n/a
45	chr3:47823524-47823574	Hela-S3	cervix:	n/a
46	chr3:47823531-47823581	NHBE	bronchial:	n/a
47	chr3:47823531-47823581	HRCEpiC	kidney:	n/a
48	chr3:47823524-47823574	RPTEC	kidney:	n/a
49	chr3:47823531-47823581	HCT-116	colon:	n/a
50	chr3:47823531-47823581	HRPEpiC	eye:	n/a

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47809506..47818715-chr3:47820075..47824996,15	MCF-7	breast:
2	chr3:47822911..47823824-chr6:136610140..136610954,2	Hela-S3	cervix:
3	chr1:110527265..110527945-chr3:47823077..47824066,2	Hela-S3	cervix:
4	chr17:70588474..70589204-chr3:47822988..47823742,2	HCT-116	colon:
5	chr15:45878972..45879914-chr3:47822992..47823712,2	Hela-S3	cervix:
6	chr3:47555041..47556961-chr3:47821638..47825112,3	MCF-7	breast:
7	chr2:10262084..10262617-chr3:47822855..47823557,2	Hela-S3	cervix:
8	chr3:47821014..47824119-chr3:47842599..47847365,10	K562	blood:
9	chr3:47821496..47825290-chr3:47843622..47845759,4	MCF-7	breast:
10	chr3:47819738..47825460-chr3:47843094..47847845,6	K562	blood:
11	chr3:47139097..47140627-chr3:47822792..47824576,2	K562	blood:
12	chr3:47823164..47824038-chr3:187871696..187872523,2	Hela-S3	cervix:
13	chr3:47823020..47823962-chr6:43597169..43598056,2	Hela-S3	cervix:
14	chr3:47553771..47557534-chr3:47822005..47824702,4	K562	blood:
15	chr3:47617723..47621182-chr3:47821900..47825077,3	MCF-7	breast:
16	chr3:47787198..47789332-chr3:47822441..47824997,2	K562	blood:
17	chr3:47821442..47824826-chr3:47842672..47846080,5	MCF-7	breast:
18	chr20:49346523..49348276-chr3:47822543..47824569,2	MCF-7	breast:
19	chr3:47821721..47824833-chr3:47865723..47867890,4	K562	blood:
20	chr3:47555068..47558623-chr3:47821026..47823771,5	K562	blood:
21	chr3:47579787..47581854-chr3:47822138..47824570,2	K562	blood:
22	chr3:47819996..47824833-chr3:47866390..47869916,6	K562	blood:

No data

Variant related genes	Relation type
SMARCC1	TF binding region
SMARCC1	CpG island
ENSG00000173473	Chromatin interaction
ENSG00000132153	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000145012	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000029363	Chromatin interaction
ENSG00000114646	Chromatin interaction
ENSG00000168710	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000270959	Chromatin interaction
ENSG00000266443	Chromatin interaction
ENSG00000266457	Chromatin interaction
ENSG00000181555	Chromatin interaction
ENSG00000260170	Chromatin interaction
ENSG00000227036	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
6	nsv965333	chr3:47815622-47845296	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv3402580	chr3:47822248-47824246	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv10270	chr3:47822606-47845578	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47820000-47825200	Active TSS	GM12878-XiMat	blood
2	chr3:47820600-47823800	Active TSS	Fetal Brain Male	brain
3	chr3:47820800-47823800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:47820800-47824000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:47820800-47824200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:47821000-47824200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:47821000-47824200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:47821000-47824600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:47821200-47823600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:47821200-47823800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:47821200-47823800	Active TSS	Fetal Intestine Large	intestine
12	chr3:47821200-47823800	Active TSS	HMEC	breast
13	chr3:47821200-47823800	Active TSS	HSMMtube	muscle
14	chr3:47821200-47824000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:47821200-47824000	Active TSS	Fetal Brain Female	brain
16	chr3:47821200-47824000	Active TSS	Thymus	Thymus
17	chr3:47821200-47824000	Active TSS	NHDF-Ad	bronchial
18	chr3:47821200-47824200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr3:47821200-47824200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:47821200-47824200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:47821200-47824400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:47821200-47824400	Active TSS	NHLF	lung
23	chr3:47821400-47823800	Active TSS	Muscle Satellite Cultured Cells	--
24	chr3:47821400-47823800	Active TSS	Fetal Intestine Small	intestine
25	chr3:47821400-47823800	Active TSS	Fetal Lung	lung
26	chr3:47821400-47823800	Active TSS	NH-A	brain
27	chr3:47821400-47824000	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:47821400-47824000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:47821400-47824200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:47821400-47824200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:47821400-47824200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:47821400-47824200	Active TSS	Fetal Stomach	stomach
33	chr3:47821400-47824400	Active TSS	A549	lung
34	chr3:47821400-47824600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:47821400-47824600	Active TSS	Colonic Mucosa	Colon
36	chr3:47821400-47824600	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr3:47821600-47823600	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr3:47821600-47823600	Active TSS	Stomach Smooth Muscle	stomach
39	chr3:47821600-47823800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:47821600-47823800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:47821600-47823800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:47821600-47823800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:47821600-47823800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:47821600-47823800	Active TSS	Hela-S3	cervix
45	chr3:47821600-47823800	Active TSS	HUVEC	blood vessel
46	chr3:47821600-47824000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:47821600-47824000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:47821600-47824000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr3:47821600-47824000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr3:47821600-47824000	Active TSS	Duodenum Mucosa	Duodenum

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