Variant report

Variant	rs172424
Chromosome Location	chr11:18022950-18022951
allele	G/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	chr11:18022135-18022984	HepG2	liver:	n/a	n/a
2	MXI1	chr11:18022278-18023127	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SERGEF	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10488683	0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10766450	0.87[EUR][1000 genomes]
rs12277387	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12292915	0.96[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs1401166	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1914710	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2108977	0.87[EUR][1000 genomes]
rs211095	0.83[YRI][hapmap]
rs211096	0.83[YRI][hapmap]
rs211114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs211135	1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211139	0.87[ASN][1000 genomes]
rs211140	0.82[YRI][hapmap]
rs211141	0.92[YRI][hapmap]
rs2137777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237919	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2237923	0.95[CEU][hapmap]
rs2283238	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2283240	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs2299623	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2679116	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs371589	1.00[CEU][hapmap]
rs3741200	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741201	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3741202	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3958112	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4757603	0.96[CEU][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4757607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs484616	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs757410	0.82[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs172424	SAAL1	cis	cerebellum	SCAN
rs172424	RP1-59M18.2	cis	Adipose Subcutaneous	GTEx
rs172424	SAAL1	cis	lymphoblastoid	seeQTL
rs172424	KCNC1	cis	parietal	SCAN
rs172424	SERGEF	cis	Adipose Subcutaneous	GTEx
rs172424	SAAL1	cis	parietal	SCAN
rs172424	SERGEF	cis	Muscle Skeletal	GTEx
rs172424	RP1-59M18.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
2	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
6	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
7	chr11:17989400-18023400	Weak transcription	Gastric	stomach
8	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
9	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
12	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:18007000-18029200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18008200-18025800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:18008200-18033200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:18008400-18023800	Weak transcription	Fetal Lung	lung
18	chr11:18008400-18026800	Weak transcription	NH-A	brain
19	chr11:18008600-18033600	Weak transcription	NHDF-Ad	bronchial
20	chr11:18008800-18025800	Weak transcription	NHEK	skin
21	chr11:18008800-18033400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:18008800-18033400	Weak transcription	HUVEC	blood vessel
23	chr11:18009200-18026200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:18009200-18026800	Weak transcription	K562	blood
25	chr11:18009400-18033600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:18010200-18033600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:18010400-18033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:18010600-18026000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:18013800-18029400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:18014200-18028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:18014200-18028600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:18014200-18029000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:18014200-18029200	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:18014200-18029800	Strong transcription	Primary T cells from cord blood	blood
35	chr11:18014600-18028000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr11:18014600-18028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:18014800-18033200	Weak transcription	Stomach Mucosa	stomach
38	chr11:18015200-18033400	Weak transcription	Fetal Heart	heart
39	chr11:18015400-18027400	Weak transcription	Hela-S3	cervix
40	chr11:18016000-18025000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:18016200-18026400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:18016200-18028800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:18016400-18033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr11:18016800-18023800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:18017000-18023400	Weak transcription	Fetal Muscle Leg	muscle
46	chr11:18017000-18025600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:18017000-18027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:18017000-18033600	Weak transcription	NHLF	lung
49	chr11:18017400-18025800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:18017600-18025200	Weak transcription	Fetal Stomach	stomach

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