Variant report

Variant	rs903147
Chromosome Location	chr4:120988116-120988117
allele	A/C
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	SP1	chr4:120987774-120988416	GM12878	blood:	n/a	n/a
2	GTF2B	chr4:120987618-120988191	K562	blood:	n/a	n/a
3	POLR2A	chr4:120987658-120988490	H1-neurons	neurons:	n/a	n/a
4	RFX5	chr4:120987557-120988754	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr4:120987682-120988836	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr4:120987724-120988877	A549	lung:	n/a	chr4:120988325-120988332
7	MAFF	chr4:120988006-120988509	K562	blood:	n/a	n/a
8	NFIC	chr4:120987343-120988574	GM12878	blood:	n/a	n/a
9	TAF1	chr4:120987495-120988748	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr4:120987523-120988742	HepG2	liver:	n/a	n/a
11	BACH1	chr4:120987522-120988157	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr4:120987664-120988297	PFSK-1	brain:	n/a	n/a
13	HA-E2F1	chr4:120987389-120988691	MCF-7	breast:	n/a	chr4:120988011-120988020
14	POLR2A	chr4:120987441-120988761	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr4:120987387-120988782	GM12892	blood:	n/a	n/a
16	POLR2A	chr4:120987496-120988778	ProgFib	skin:	n/a	n/a
17	MAX	chr4:120987378-120988848	A549	lung:	n/a	n/a
18	GABPA	chr4:120987435-120988847	MCF-7	breast:	n/a	chr4:120988010-120988024 chr4:120988007-120988021 chr4:120988010-120988019 chr4:120988010-120988021
19	MAX	chr4:120987154-120988535	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:120987516-120988954	GM12878	blood:	n/a	n/a
21	TAF1	chr4:120987495-120988771	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr4:120986908-120989985	GM12891	blood:	n/a	n/a
23	POLR2A	chr4:120987337-120989347	GM19099	blood:	n/a	n/a
24	FOXM1	chr4:120987550-120988461	ECC-1	luminal epithelium:	n/a	n/a
25	E2F4	chr4:120987567-120988340	GM12878	blood:	n/a	chr4:120987957-120987968 chr4:120988011-120988020
26	NRF1	chr4:120987837-120988821	K562	blood:	n/a	chr4:120988010-120988024 chr4:120988007-120988021 chr4:120988009-120988020 chr4:120988010-120988019 chr4:120988010-120988021
27	MBD4	chr4:120988073-120988951	HepG2	liver:	n/a	n/a
28	POLR2A	chr4:120987476-120988284	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr4:120987736-120988246	SK-N-SH	brain:	n/a	n/a
30	CREB1	chr4:120987728-120988517	K562	blood:	n/a	n/a
31	REST	chr4:120987731-120988163	PFSK-1	brain:	n/a	n/a
32	EP300	chr4:120987841-120988576	GM12878	blood:	n/a	chr4:120988036-120988052
33	HDAC2	chr4:120987492-120988702	MCF-7	breast:	n/a	chr4:120987498-120987512 chr4:120987503-120987517 chr4:120987501-120987515 chr4:120987499-120987513 chr4:120987500-120987514
34	POLR2A	chr4:120987175-120989426	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:120987221-120988829	K562	blood:	n/a	n/a
36	MAX	chr4:120987276-120988610	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:120987396-120989166	GM12892	blood:	n/a	n/a
38	POLR2A	chr4:120987579-120988715	A549	lung:	n/a	n/a
39	REST	chr4:120987589-120988247	SK-N-SH	brain:	n/a	n/a
40	YY1	chr4:120987552-120988223	K562	blood:	n/a	n/a
41	POU2F2	chr4:120987794-120988484	GM12878	blood:	n/a	n/a
42	ZEB1	chr4:120987935-120988427	GM12878	blood:	n/a	n/a
43	SIN3AK20	chr4:120987572-120988232	PFSK-1	brain:	n/a	n/a
44	REST	chr4:120987672-120988281	A549	lung:	n/a	n/a
45	ZBTB33	chr4:120987983-120988198	HCT-116	colon:	n/a	chr4:120988079-120988094 chr4:120988085-120988095
46	USF2	chr4:120987846-120988539	H1-hESC	embryonic stem cell:	n/a	chr4:120988344-120988355
47	POLR2A	chr4:120987270-120989178	PFSK-1	brain:	n/a	n/a
48	CREB1	chr4:120987580-120988188	A549	lung:	n/a	n/a
49	ELF1	chr4:120987793-120988797	HepG2	liver:	n/a	n/a
50	POLR2A	chr4:120987653-120988666	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:
2	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
3	chr4:120548759..120550296-chr4:120986622..120988750,2	K562	blood:
4	chr4:120987081..120989411-chr4:129732197..129734433,2	K562	blood:
5	chr4:120131661..120133788-chr4:120986266..120989312,3	K562	blood:
6	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
7	chr4:120988053..120988648-chr8:22298298..22298997,2	Hela-S3	cervix:
8	chr14:34419791..34420629-chr4:120987839..120988645,2	Hela-S3	cervix:
9	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:
10	chr1:89990056..89990615-chr4:120987741..120988260,2	HCT-116	colon:
11	chr1:222885721..222886410-chr4:120987809..120988640,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-6	chr4:120988015-120991623	NONHSAT098115
2	lnc-AC110373.1-6	chr4:120988113-120988156	ENSG00000250938.1
3	lnc-AC110373.1-6	chr4:120988113-120988156	ENSG00000250938.1

Variant related genes	Relation type
ENSG00000250938	TF binding region
MAD2L1	TF binding region
ENSG00000269893	Chromatin interaction
ENSG00000197147	Chromatin interaction
ENSG00000129521	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000162819	Chromatin interaction
ENSG00000164096	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000138735	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000120910	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10010446	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1075717	0.80[ASN][1000 genomes]
rs11942060	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12711084	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1972014	0.84[ASN][1000 genomes]
rs28538838	0.84[ASN][1000 genomes]
rs2904883	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904884	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2908990	0.83[ASN][1000 genomes]
rs2934379	0.84[ASN][1000 genomes]
rs4834834	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534168	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 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	chr4:120985800-120988600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120985800-120988800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr4:120986000-120988800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:120986000-120988800	Active TSS	HMEC	breast
5	chr4:120986000-120989000	Active TSS	A549	lung
6	chr4:120986000-120989200	Active TSS	K562	blood
7	chr4:120986400-120988800	Active TSS	Hela-S3	cervix
8	chr4:120986400-120989000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:120986400-120989000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:120986400-120989000	Active TSS	NHDF-Ad	bronchial
11	chr4:120986400-120989200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:120986400-120989200	Active TSS	GM12878-XiMat	blood
13	chr4:120986400-120989400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr4:120986600-120988800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr4:120986600-120988800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:120986600-120989000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:120986600-120989000	Active TSS	Thymus	Thymus
18	chr4:120986600-120989000	Active TSS	NHLF	lung
19	chr4:120986800-120988800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:120986800-120988800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:120986800-120988800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:120986800-120988800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:120986800-120988800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:120986800-120989000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr4:120986800-120989400	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr4:120986800-120989800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr4:120987000-120988800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:120987000-120988800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:120987000-120988800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr4:120987000-120988800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:120987000-120988800	Active TSS	Fetal Intestine Large	intestine
32	chr4:120987000-120988800	Active TSS	Fetal Kidney	kidney
33	chr4:120987000-120988800	Active TSS	NHEK	skin
34	chr4:120987000-120989000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:120987000-120989000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:120987000-120989000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:120987000-120989000	Active TSS	Dnd41	blood
38	chr4:120987000-120989000	Active TSS	HSMM	muscle
39	chr4:120987000-120989600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:120987200-120988800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:120987200-120988800	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr4:120987200-120988800	Active TSS	Esophagus	oesophagus
43	chr4:120987200-120988800	Active TSS	Gastric	stomach
44	chr4:120987200-120988800	Active TSS	Rectal Smooth Muscle	rectum
45	chr4:120987200-120989000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr4:120987200-120989000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:120987200-120989000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:120987200-120989000	Active TSS	Colonic Mucosa	Colon
49	chr4:120987200-120989000	Active TSS	HSMMtube	muscle
50	chr4:120987200-120989200	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links