Variant report

Variant	rs1488940
Chromosome Location	chr4:56412489-56412490
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	POLR2A	chr4:56411760-56413743	GM12892	blood:	n/a	n/a
2	POLR2A	chr4:56411805-56413785	HEK293	kidney:	n/a	n/a
3	E2F6	chr4:56411907-56412733	K562	blood:	n/a	chr4:56412368-56412380 chr4:56412371-56412380
4	PML	chr4:56411494-56412602	GM12878	blood:	n/a	chr4:56412040-56412048
5	POLR2A	chr4:56411885-56412574	GM12891	blood:	n/a	n/a
6	UBTF	chr4:56411790-56413671	K562	blood:	n/a	n/a
7	MYC	chr4:56411836-56413935	NB4	blood:	n/a	n/a
8	POLR2A	chr4:56411907-56413438	HepG2	liver:	n/a	n/a
9	TAF1	chr4:56411772-56412519	SK-N-SH	brain:	n/a	n/a
10	MAX	chr4:56411798-56413489	K562	blood:	n/a	n/a
11	POLR2A	chr4:56412415-56413364	A549	lung:	n/a	n/a
12	MAX	chr4:56411853-56412778	SK-N-SH	brain:	n/a	n/a
13	CEBPD	chr4:56412451-56413365	HepG2	liver:	n/a	n/a
14	MYC	chr4:56411994-56412600	HepG2	liver:	n/a	n/a
15	BHLHE40	chr4:56411798-56412519	HepG2	liver:	n/a	chr4:56412373-56412389 chr4:56412397-56412413
16	POLR2A	chr4:56411837-56413463	K562	blood:	n/a	n/a
17	TCF3	chr4:56411973-56412498	GM12878	blood:	n/a	chr4:56412471-56412484
18	POLR2A	chr4:56411856-56413761	GM18526	blood:	n/a	n/a
19	CTCF	chr4:56412420-56412570	HMEC	breast:	n/a	n/a
20	POLR2A	chr4:56411863-56413580	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:56411411-56413548	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr4:56411691-56412490	HUVEC	blood vessel:	n/a	n/a
23	TCF12	chr4:56411856-56413602	ECC-1	luminal epithelium:	n/a	chr4:56412471-56412481
24	EP300	chr4:56411688-56413646	SK-N-SH	brain:	n/a	chr4:56412374-56412390 chr4:56412075-56412091
25	POLR2A	chr4:56411827-56413502	K562	blood:	n/a	n/a
26	POLR2A	chr4:56411764-56412641	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr4:56411822-56413831	GM18505	blood:	n/a	n/a
28	CHD2	chr4:56411971-56413558	GM12878	blood:	n/a	chr4:56412052-56412062
29	TCF3	chr4:56412273-56412595	GM12878	blood:	n/a	chr4:56412471-56412484
30	POLR2A	chr4:56411697-56413694	K562	blood:	n/a	n/a
31	CHD2	chr4:56411727-56413487	K562	blood:	n/a	chr4:56412052-56412062
32	POLR2A	chr4:56411795-56412755	ECC-1	luminal epithelium:	n/a	n/a
33	MTA3	chr4:56411580-56412639	GM12878	blood:	n/a	n/a
34	MAX	chr4:56411872-56412676	MCF-7	breast:	n/a	n/a
35	TCF7L2	chr4:56411497-56413490	HCT-116	colon:	n/a	n/a
36	POLR2A	chr4:56411870-56413431	GM10847	blood:	n/a	n/a
37	REST	chr4:56411851-56414060	H1-neurons	neurons:	n/a	n/a
38	CTCF	chr4:56412400-56412550	Caco-2	colon:	n/a	n/a
39	POLR2A	chr4:56411682-56413984	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr4:56411684-56412764	U87	brain:	n/a	n/a
41	MYC	chr4:56411776-56413367	K562	blood:	n/a	n/a
42	BHLHE40	chr4:56411869-56413630	GM12878	blood:	n/a	chr4:56412373-56412389 chr4:56412397-56412413
43	POLR2A	chr4:56411988-56413451	A549	lung:	n/a	n/a
44	YY1	chr4:56411783-56412526	K562	blood:	n/a	chr4:56412449-56412460 chr4:56412248-56412262
45	CTCF	chr4:56412340-56412490	NHEK	skin:	n/a	n/a
46	CHD2	chr4:56411801-56413628	Hela-S3	cervix:	n/a	chr4:56412052-56412062 chr4:56413593-56413600
47	POLR2A	chr4:56411987-56412577	GM12891	blood:	n/a	n/a
48	POLR2A	chr4:56411788-56413610	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr4:56411920-56413779	A549	lung:	n/a	n/a
50	POLR2A	chr4:56411879-56412549	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56403772..56408020-chr4:56410640..56413640,7	MCF-7	breast:
2	chr4:56412226..56412922-chr9:86594760..86595405,2	HCT-116	colon:
3	chr19:41196036..41196567-chr4:56412258..56412956,2	Hela-S3	cervix:
4	chr4:56212143..56212708-chr4:56412445..56413440,2	Hela-S3	cervix:
5	chr4:56410839..56413778-chr4:56501227..56505067,4	K562	blood:
6	chr4:56343066..56345734-chr4:56411419..56413594,3	MCF-7	breast:
7	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
8	chr4:56412302..56413038-chr5:141704186..141705186,2	HCT-116	colon:
9	chr4:56412329..56414161-chr4:56494486..56496762,2	K562	blood:
10	chr4:56411581..56413941-chr4:57300856..57302618,2	K562	blood:
11	chr4:56275450..56278290-chr4:56412391..56414503,2	K562	blood:
12	chr4:56411599..56413538-chr4:56502547..56504625,2	MCF-7	breast:
13	chr4:56408119..56414507-chr4:56501105..56505595,8	K562	blood:

Variant related genes	Relation type
CLOCK	TF binding region
ENSG00000272969	TF binding region
ENSG00000187678	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000109255	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000223305	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000231185	Chromatin interaction
ENSG00000203615	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10031586	1.00[EUR][1000 genomes]
rs1533803	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1554482	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17085739	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17085769	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17085780	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17085821	1.00[EUR][1000 genomes]
rs2130039	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2140076	1.00[EUR][1000 genomes]
rs2412660	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35150421	1.00[EUR][1000 genomes]
rs57219525	1.00[EUR][1000 genomes]
rs57848550	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58395965	1.00[EUR][1000 genomes]
rs6820823	1.00[EUR][1000 genomes]
rs6847415	1.00[EUR][1000 genomes]
rs6855837	1.00[EUR][1000 genomes]
rs73149762	1.00[EUR][1000 genomes]
rs73151873	1.00[EUR][1000 genomes]
rs73151889	1.00[EUR][1000 genomes]
rs73153687	1.00[EUR][1000 genomes]
rs73817206	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819624	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819626	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819631	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819633	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819635	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819636	0.85[AFR][1000 genomes]
rs73819642	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73819647	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7655255	1.00[EUR][1000 genomes]
rs7693751	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3439567	chr4:56411220-56414568	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
5	esv3433892	chr4:56411745-56413843	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56410400-56413600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:56410400-56413800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56410400-56414000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:56410600-56413600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:56410600-56413600	Active TSS	K562	blood
6	chr4:56410800-56413600	Active TSS	Duodenum Mucosa	Duodenum
7	chr4:56410800-56413800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr4:56410800-56413800	Active TSS	Fetal Intestine Large	intestine
9	chr4:56410800-56413800	Active TSS	Hela-S3	cervix
10	chr4:56410800-56414200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:56410800-56414200	Active TSS	NHLF	lung
12	chr4:56411000-56413600	Active TSS	HMEC	breast
13	chr4:56411000-56413600	Active TSS	NHEK	skin
14	chr4:56411000-56413800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr4:56411000-56413800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr4:56411000-56413800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:56411000-56413800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:56411000-56413800	Active TSS	GM12878-XiMat	blood
19	chr4:56411000-56413800	Active TSS	NH-A	brain
20	chr4:56411000-56414000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:56411000-56414000	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr4:56411000-56414000	Active TSS	A549	lung
23	chr4:56411000-56414200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:56411000-56414200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:56411000-56414200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:56411000-56414400	Active TSS	Fetal Brain Female	brain
27	chr4:56411200-56412600	Active TSS	Right Atrium	heart
28	chr4:56411200-56413400	Active TSS	Colonic Mucosa	Colon
29	chr4:56411200-56413600	Active TSS	Fetal Intestine Small	intestine
30	chr4:56411200-56413600	Active TSS	Pancreas	Pancrea
31	chr4:56411200-56413800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:56411200-56413800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:56411200-56413800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr4:56411200-56413800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:56411200-56413800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr4:56411200-56413800	Active TSS	Muscle Satellite Cultured Cells	--
37	chr4:56411200-56413800	Active TSS	Fetal Kidney	kidney
38	chr4:56411200-56413800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr4:56411200-56413800	Active TSS	Rectal Smooth Muscle	rectum
40	chr4:56411200-56413800	Active TSS	HSMM	muscle
41	chr4:56411200-56414000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr4:56411200-56414000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:56411200-56414000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:56411200-56414000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:56411200-56414000	Active TSS	NHDF-Ad	bronchial
46	chr4:56411200-56414400	Active TSS	Brain Germinal Matrix	brain
47	chr4:56411200-56414600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr4:56411400-56412600	Bivalent/Poised TSS	Thymus	Thymus
49	chr4:56411400-56413400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:56411400-56413400	Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links