Variant report

Variant	rs11023934
Chromosome Location	chr11:16425958-16425959
allele	A/T
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	FOXA2	chr11:16425306-16426083	HepG2	liver:	n/a	chr11:16425713-16425725

Variant related genes	Relation type
SOX6	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1004283	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10500830	0.94[CEU][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10741698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766325	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766327	0.84[EUR][1000 genomes]
rs10832601	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832602	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832603	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10832616	0.85[EUR][1000 genomes]
rs10832617	0.85[EUR][1000 genomes]
rs10832619	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10832620	0.84[EUR][1000 genomes]
rs10832624	0.84[EUR][1000 genomes]
rs10832625	0.84[EUR][1000 genomes]
rs10832626	0.84[EUR][1000 genomes]
rs11023932	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11023940	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11023942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11023943	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11023947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11023964	0.84[EUR][1000 genomes]
rs11023965	0.84[EUR][1000 genomes]
rs11023969	0.84[EUR][1000 genomes]
rs11023971	0.84[EUR][1000 genomes]
rs11529135	0.84[EUR][1000 genomes]
rs11529591	0.84[EUR][1000 genomes]
rs11605526	0.82[EUR][1000 genomes]
rs12221729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221945	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12221946	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12222249	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1393924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1393926	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1503440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16933105	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16933117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134610	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2174164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297325	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs297332	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259791	0.84[EUR][1000 genomes]
rs4491181	0.84[EUR][1000 genomes]
rs4550186	0.84[EUR][1000 genomes]
rs4756850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757399	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757403	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61881805	0.85[EUR][1000 genomes]
rs61881829	0.84[EUR][1000 genomes]
rs61881830	0.84[EUR][1000 genomes]
rs61883215	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7483029	0.84[EUR][1000 genomes]
rs7926068	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935820	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9666320	0.83[EUR][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16417200-16434200	Weak transcription	Psoas Muscle	Psoas
2	chr11:16423600-16428000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:16423800-16428200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr11:16424000-16427400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:16424000-16428000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:16424200-16427400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr11:16424400-16426000	Enhancers	Fetal Intestine Large	intestine
8	chr11:16424400-16426200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:16424400-16426400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:16424400-16426800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:16424400-16426800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr11:16424400-16427200	Enhancers	Fetal Intestine Small	intestine
13	chr11:16424800-16426800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:16424800-16428000	Enhancers	HepG2	liver
15	chr11:16425000-16427000	Enhancers	Duodenum Mucosa	Duodenum
16	chr11:16425000-16427200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:16425200-16426000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr11:16425200-16426000	Weak transcription	Brain Substantia Nigra	brain
19	chr11:16425200-16426800	Enhancers	Brain Hippocampus Middle	brain
20	chr11:16425200-16427600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr11:16425200-16428000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
22	chr11:16425200-16428000	Weak transcription	K562	blood
23	chr11:16425400-16426200	Weak transcription	Brain Germinal Matrix	brain
24	chr11:16425400-16426600	Weak transcription	Fetal Kidney	kidney
25	chr11:16425600-16426200	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr11:16425600-16427000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr11:16425600-16427200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr11:16425800-16426800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:16425800-16427000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:16425800-16427600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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