Variant report

Variant	rs2513508
Chromosome Location	chr11:76234528-76234529
allele	C/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	FOXA1	chr11:76234179-76234638	HepG2	liver:	n/a	n/a
2	FOXA1	chr11:76234207-76234571	HepG2	liver:	n/a	n/a
3	FOXA1	chr11:76234173-76234600	HepG2	liver:	n/a	n/a
4	FOXA1	chr11:76234171-76234595	HepG2	liver:	n/a	n/a
5	FOXA2	chr11:76234179-76234551	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
C11orf30	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10160382	0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1044265	0.93[ASW][hapmap]
rs10793167	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs10793169	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10793171	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10899217	0.80[EUR][1000 genomes]
rs10899222	0.83[EUR][1000 genomes]
rs10899225	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10899227	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11606394	0.93[ASW][hapmap];0.83[YRI][hapmap]
rs17749618	0.81[CEU][hapmap]
rs1939467	0.85[CEU][hapmap]
rs1939468	0.81[CEU][hapmap]
rs2251075	0.83[YRI][hapmap]
rs2508740	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2508741	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2508753	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2508756	0.93[ASW][hapmap];0.83[YRI][hapmap]
rs2508759	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508760	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2508761	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2508762	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2513504	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2513505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2513513	1.00[ASW][hapmap];0.96[CEU][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];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513515	0.83[YRI][hapmap]
rs2513520	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2513523	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513525	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3753051	0.81[CEU][hapmap]
rs3814711	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4245443	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4272809	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4300410	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4625500	0.82[YRI][hapmap]
rs4945087	0.80[ASW][hapmap];0.83[YRI][hapmap]
rs4945090	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5023625	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55977477	0.83[EUR][1000 genomes]
rs7106564	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7107058	0.93[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7123361	0.88[CEU][hapmap]
rs7125552	0.85[CEU][hapmap]
rs7926009	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs7942257	0.81[CEU][hapmap]
rs7949258	0.85[CEU][hapmap]
rs8848	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050713	chr11:76147085-76267117	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2513508	ALG8	cis	cerebellum	SCAN
rs2513508	ARRB1	cis	parietal	SCAN
rs2513508	ARHGEF17	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76168800-76234800	Weak transcription	Psoas Muscle	Psoas
2	chr11:76184400-76235000	Weak transcription	NHEK	skin
3	chr11:76191400-76239000	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:76192800-76242800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:76205200-76235800	Weak transcription	NHLF	lung
6	chr11:76205200-76254400	Weak transcription	Aorta	Aorta
7	chr11:76205400-76235800	Weak transcription	Lung	lung
8	chr11:76205400-76240000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:76205400-76254600	Weak transcription	Right Ventricle	heart
10	chr11:76205400-76255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:76205600-76239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:76205800-76235800	Weak transcription	Esophagus	oesophagus
13	chr11:76206000-76249200	Weak transcription	Colonic Mucosa	Colon
14	chr11:76207400-76239400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:76207400-76240000	Weak transcription	Brain Substantia Nigra	brain
16	chr11:76207400-76254400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:76207600-76239400	Weak transcription	Brain Angular Gyrus	brain
18	chr11:76208000-76235200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:76212000-76235200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr11:76212000-76235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:76212800-76235000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:76213000-76237200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:76213000-76254200	Weak transcription	Fetal Heart	heart
24	chr11:76213200-76235200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:76214400-76234800	Weak transcription	Fetal Intestine Small	intestine
26	chr11:76218600-76234600	Weak transcription	Brain Germinal Matrix	brain
27	chr11:76219800-76234800	Weak transcription	Fetal Brain Female	brain
28	chr11:76220000-76255600	Weak transcription	Small Intestine	intestine
29	chr11:76220400-76234800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:76221800-76234600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:76221800-76235600	Weak transcription	Gastric	stomach
32	chr11:76221800-76235800	Weak transcription	Pancreas	Pancrea
33	chr11:76222200-76252800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr11:76222600-76249200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:76224200-76235200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:76224200-76239000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:76224200-76254600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr11:76224400-76236000	Weak transcription	Spleen	Spleen
39	chr11:76224400-76262600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:76224400-76263800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:76224800-76251200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:76225400-76253200	Weak transcription	HSMMtube	muscle
43	chr11:76226800-76235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:76227000-76236000	Weak transcription	A549	lung
45	chr11:76229000-76234600	Weak transcription	HSMM	muscle
46	chr11:76229000-76235200	Weak transcription	Hela-S3	cervix
47	chr11:76229000-76235200	Weak transcription	NH-A	brain
48	chr11:76229000-76235600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:76229000-76239800	Weak transcription	HUVEC	blood vessel
50	chr11:76229600-76238200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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