Variant report

Variant	rs11953558
Chromosome Location	chr5:115913205-115913206
allele	C/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	PAX5	chr5:115912622-115913427	GM12878	blood:	n/a	n/a
2	CREB1	chr5:115912213-115913459	GM12878	blood:	n/a	n/a
3	MEF2A	chr5:115912719-115913249	GM12878	blood:	n/a	chr5:115913095-115913110 chr5:115913095-115913112 chr5:115913097-115913108 chr5:115913095-115913110 chr5:115913097-115913112
4	TCF12	chr5:115912713-115913290	GM12878	blood:	n/a	n/a
5	BCL3	chr5:115912689-115913278	GM12878	blood:	n/a	n/a
6	RUNX3	chr5:115912509-115913584	GM12878	blood:	n/a	n/a
7	TCF7L2	chr5:115912895-115913245	HEK293	kidney:	n/a	chr5:115913003-115913017 chr5:115913006-115913015 chr5:115913006-115913016 chr5:115913006-115913013
8	EBF1	chr5:115912634-115913390	GM12878	blood:	n/a	chr5:115912875-115912886 chr5:115912878-115912887
9	IKZF1	chr5:115912479-115913395	GM12878	blood:	n/a	n/a
10	EP300	chr5:115912408-115913440	GM12878	blood:	n/a	n/a
11	MXI1	chr5:115912432-115913371	GM12878	blood:	n/a	n/a
12	BHLHE40	chr5:115912580-115913446	GM12878	blood:	n/a	n/a
13	EP300	chr5:115912643-115913279	GM12878	blood:	n/a	n/a
14	EP300	chr5:115911664-115913404	GM12878	blood:	n/a	n/a
15	EBF1	chr5:115912645-115913406	GM12878	blood:	n/a	chr5:115912875-115912886 chr5:115912878-115912887
16	NFATC1	chr5:115912678-115913358	GM12878	blood:	n/a	n/a
17	YY1	chr5:115912709-115913291	GM12878	blood:	n/a	n/a
18	RELA	chr5:115912737-115913331	GM10847	blood:	n/a	n/a
19	CHD2	chr5:115911292-115913493	GM12878	blood:	n/a	n/a
20	ZNF384	chr5:115912776-115913344	GM12878	blood:	n/a	n/a
21	YY1	chr5:115912791-115913304	GM12878	blood:	n/a	n/a
22	WRNIP1	chr5:115912695-115913511	GM12878	blood:	n/a	n/a
23	MAZ	chr5:115911249-115913425	GM12878	blood:	n/a	chr5:115912792-115912807 chr5:115912793-115912802 chr5:115912792-115912805 chr5:115912794-115912804 chr5:115911492-115911502 chr5:115912794-115912803 chr5:115912792-115912805 chr5:115912794-115912803 chr5:115912793-115912804 chr5:115912792-115912805 chr5:115912790-115912805 chr5:115912792-115912805 chr5:115912793-115912804 chr5:115912793-115912803
24	RAD21	chr5:115911613-115913432	GM12878	blood:	n/a	chr5:115911934-115911953
25	SP1	chr5:115912674-115913377	GM12878	blood:	n/a	n/a
26	ATF2	chr5:115912607-115913221	H1-hESC	embryonic stem cell:	n/a	chr5:115913109-115913120
27	NRF1	chr5:115913157-115913218	GM12878	blood:	n/a	n/a
28	PAX5	chr5:115912753-115913268	GM12878	blood:	n/a	n/a
29	RELA	chr5:115912726-115913333	GM15510	blood:	n/a	n/a
30	RFX5	chr5:115912827-115913466	GM12878	blood:	n/a	n/a
31	EBF1	chr5:115910383-115913484	GM12878	blood:	n/a	chr5:115912875-115912886 chr5:115912878-115912887
32	RCOR1	chr5:115911602-115913462	GM12878	blood:	n/a	n/a
33	BCLAF1	chr5:115912568-115913383	GM12878	blood:	n/a	n/a
34	RAD21	chr5:115912770-115913337	GM12878	blood:	n/a	n/a
35	MTA3	chr5:115911889-115913511	GM12878	blood:	n/a	n/a
36	STAT3	chr5:115912468-115913323	GM12878	blood:	n/a	chr5:115913041-115913052
37	RELA	chr5:115912698-115913329	GM18505	blood:	n/a	n/a
38	BCLAF1	chr5:115912628-115913360	GM12878	blood:	n/a	n/a
39	POU2F2	chr5:115912661-115913512	GM12878	blood:	n/a	n/a
40	RELA	chr5:115912710-115913364	GM18526	blood:	n/a	n/a
41	POLR2A	chr5:115910283-115913382	GM12878	blood:	n/a	n/a
42	FOXM1	chr5:115912572-115913427	GM12878	blood:	n/a	n/a
43	STAT1	chr5:115912737-115913347	GM12878	blood:	n/a	chr5:115913041-115913052
44	ATF2	chr5:115912396-115913473	GM12878	blood:	n/a	chr5:115913109-115913120
45	BCL11A	chr5:115912734-115913315	GM12878	blood:	n/a	n/a
46	CHD1	chr5:115910361-115913446	GM12878	blood:	n/a	n/a
47	FOXM1	chr5:115911651-115913474	GM12878	blood:	n/a	n/a
48	PML	chr5:115911514-115913522	GM12878	blood:	n/a	n/a
49	TBP	chr5:115911752-115913404	GM12878	blood:	n/a	n/a
50	YY1	chr5:115912731-115913251	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:10764160..10766526-chr5:115912031..115913531,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region
ENSG00000267100	Chromatin interaction
ENSG00000129351	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10045872	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10053792	0.98[ASN][1000 genomes]
rs10061055	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062998	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10066922	0.98[ASN][1000 genomes]
rs10070276	0.88[ASN][1000 genomes]
rs10073289	0.83[ASN][1000 genomes]
rs10074788	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10075410	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10080023	0.98[ASN][1000 genomes]
rs1027742	0.94[ASN][1000 genomes]
rs12719220	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13354122	0.91[ASN][1000 genomes]
rs13355655	0.99[ASN][1000 genomes]
rs13357599	1.00[ASN][1000 genomes]
rs13360587	0.94[ASN][1000 genomes]
rs1345706	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1345707	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17140120	0.83[ASN][1000 genomes]
rs17140171	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17140176	0.94[ASN][1000 genomes]
rs1862372	0.97[ASN][1000 genomes]
rs1862373	0.85[ASN][1000 genomes]
rs2840113	0.94[ASN][1000 genomes]
rs28489253	0.94[ASN][1000 genomes]
rs3806914	0.99[ASN][1000 genomes]
rs3806915	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806916	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56257700	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57497884	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57557217	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58364462	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59351578	0.94[ASN][1000 genomes]
rs60783407	0.80[AMR][1000 genomes]
rs6878936	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6897765	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6898172	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73780374	0.84[ASN][1000 genomes]
rs73780375	0.84[ASN][1000 genomes]
rs9327010	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9327011	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9327012	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115911800-115914400	Weak transcription	HepG2	liver
2	chr5:115912200-115913400	Flanking Active TSS	GM12878-XiMat	blood
3	chr5:115912400-115913400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr5:115912400-115913800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:115912400-115914200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:115912400-115914600	Weak transcription	Fetal Lung	lung
7	chr5:115912400-115917800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:115912400-115930000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:115912600-115913400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:115912600-115914800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr5:115912600-115916800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:115912600-115917000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:115912800-115913600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:115912800-115914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:115912800-115915000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:115912800-115915200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:115913000-115913600	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:115913000-115913600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr5:115913000-115914000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:115913000-115914800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:115913000-115917000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:115913000-115917800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:115913000-115919000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:115913200-115914400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:115913200-115915000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:115913200-115927200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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