Variant report

Variant	rs1503441
Chromosome Location	chr11:16424655-16424656
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	JUND	chr11:16424439-16424955	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUN	chr11:16424499-16424970	H1-hESC	embryonic stem cell:	n/a	chr11:16424694-16424707
3	EP300	chr11:16423915-16424671	ECC-1	luminal epithelium:	n/a	n/a
4	SP1	chr11:16424107-16424661	HepG2	liver:	n/a	n/a
5	ARID3A	chr11:16424180-16424827	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:16424493-16424911	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr11:16424128-16425173	ECC-1	luminal epithelium:	n/a	n/a
8	SP1	chr11:16424370-16425036	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr11:16424483-16425098	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFF	chr11:16424374-16424817	HepG2	liver:	n/a	n/a
11	JUN	chr11:16424538-16424880	HepG2	liver:	n/a	chr11:16424694-16424707
12	ATF2	chr11:16424326-16425117	H1-hESC	embryonic stem cell:	n/a	n/a
13	CREB1	chr11:16424419-16425032	H1-hESC	embryonic stem cell:	n/a	n/a
14	HDAC2	chr11:16424583-16424997	H1-hESC	embryonic stem cell:	n/a	n/a
15	POU5F1	chr11:16424491-16425021	H1-hESC	embryonic stem cell:	n/a	chr11:16424766-16424780 chr11:16424712-16424726 chr11:16424712-16424726 chr11:16424765-16424779 chr11:16424766-16424780 chr11:16424712-16424726 chr11:16424766-16424780
16	POLR2A	chr11:16424501-16424797	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr11:16424599-16424926	H1-hESC	embryonic stem cell:	n/a	n/a
18	ATF2	chr11:16424453-16424972	H1-hESC	embryonic stem cell:	n/a	n/a
19	TEAD4	chr11:16424476-16425025	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF274	chr11:16424619-16424796	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP1	chr11:16424409-16425081	H1-hESC	embryonic stem cell:	n/a	n/a
22	BCL11A	chr11:16424558-16424905	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAFK	chr11:16424522-16424986	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUND	chr11:16424383-16424873	HepG2	liver:	n/a	n/a
25	EP300	chr11:16424546-16424915	H1-hESC	embryonic stem cell:	n/a	n/a
26	JUND	chr11:16424390-16425099	H1-hESC	embryonic stem cell:	n/a	n/a
27	BCL11A	chr11:16424540-16424931	H1-hESC	embryonic stem cell:	n/a	n/a
28	NFIC	chr11:16424122-16424694	HepG2	liver:	n/a	n/a
29	TCF12	chr11:16424449-16425078	H1-hESC	embryonic stem cell:	n/a	n/a
30	NANOG	chr11:16424565-16424969	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SOX6	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1000565	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1039508	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603071	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604277	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608205	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12276516	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12790582	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12793343	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805370	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12806133	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393927	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503452	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566771	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17470652	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17554835	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847315	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469046	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34737838	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34742295	0.80[ASN][1000 genomes]
rs35503644	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35944766	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66705712	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66906527	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67280587	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7930085	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932807	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7945099	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7946119	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv529731	chr11:16122782-16468170	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv553566	chr11:16329009-16799044	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv832075	chr11:16391700-16490934	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16417200-16434200	Weak transcription	Psoas Muscle	Psoas
2	chr11:16418000-16425200	Weak transcription	Brain Germinal Matrix	brain
3	chr11:16419600-16425000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:16423600-16428000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:16423800-16428200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr11:16424000-16425000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr11:16424000-16425400	Enhancers	Fetal Kidney	kidney
8	chr11:16424000-16425600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:16424000-16425800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr11:16424000-16427400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:16424000-16428000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:16424200-16425000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:16424200-16425800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:16424200-16427400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr11:16424400-16424800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr11:16424400-16424800	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr11:16424400-16424800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr11:16424400-16424800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr11:16424400-16424800	Flanking Active TSS	HepG2	liver
20	chr11:16424400-16425000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr11:16424400-16425000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:16424400-16425000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr11:16424400-16425000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr11:16424400-16425000	Enhancers	Fetal Heart	heart
25	chr11:16424400-16425200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr11:16424400-16426000	Enhancers	Fetal Intestine Large	intestine
27	chr11:16424400-16426200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:16424400-16426400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr11:16424400-16426800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:16424400-16426800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr11:16424400-16427200	Enhancers	Fetal Intestine Small	intestine
32	chr11:16424600-16424800	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr11:16424600-16425000	Active TSS	Brain Anterior Caudate	brain
34	chr11:16424600-16425000	Active TSS	Brain Substantia Nigra	brain
35	chr11:16424600-16425200	Active TSS	Brain Hippocampus Middle	brain
36	chr11:16424600-16425200	Enhancers	K562	blood

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