Variant report

Variant	rs1790404
Chromosome Location	chr11:73822134-73822135
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10898954	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898956	0.82[ASN][1000 genomes]
rs1614299	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615115	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1685326	1.00[YRI][hapmap]
rs1685355	0.86[JPT][hapmap]
rs1726735	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1726744	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1726745	0.86[JPT][hapmap]
rs1726746	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1726751	0.84[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1726752	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1726764	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs1783537	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs1790381	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790398	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790399	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2007567	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075577	0.86[JPT][hapmap]
rs3018184	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4453265	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs474280	0.89[ASW][hapmap];0.85[CHD][hapmap]
rs474835	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs486577	0.89[ASW][hapmap];0.85[CHD][hapmap]
rs490539	0.89[ASW][hapmap];0.85[CHD][hapmap]
rs4944036	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944038	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4944878	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500608	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs575096	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs588097	0.86[JPT][hapmap]
rs590336	0.86[JPT][hapmap]
rs635441	0.86[JPT][hapmap]
rs647126	0.86[JPT][hapmap]
rs6592545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592551	0.83[EUR][1000 genomes]
rs7121868	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7483884	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7926165	0.86[JPT][hapmap]
rs826033	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826039	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826056	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826061	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826062	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826066	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1790404	P4HA3	cis	Thyroid	GTEx
rs1790404	C2CD3	cis	parietal	SCAN
rs1790404	FGF19	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
2	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:73785600-73823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:73794600-73823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:73795200-73823800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:73801600-73823600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:73802000-73831800	Weak transcription	Pancreas	Pancrea
8	chr11:73802200-73880800	Weak transcription	Esophagus	oesophagus
9	chr11:73802400-73832000	Weak transcription	Fetal Heart	heart
10	chr11:73804000-73832400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:73804000-73880800	Weak transcription	Aorta	Aorta
12	chr11:73805000-73823600	Weak transcription	Colonic Mucosa	Colon
13	chr11:73808800-73823600	Weak transcription	Colon Smooth Muscle	Colon
14	chr11:73809800-73844400	Weak transcription	HMEC	breast
15	chr11:73809800-73847200	Weak transcription	HepG2	liver
16	chr11:73812000-73849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:73814600-73823800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:73814600-73845400	Weak transcription	Psoas Muscle	Psoas
19	chr11:73814800-73823800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:73814800-73824800	Weak transcription	Fetal Brain Male	brain
21	chr11:73815000-73823800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:73815000-73824800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:73815400-73834200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:73816200-73822400	Strong transcription	HSMMtube	muscle
25	chr11:73816800-73840000	Weak transcription	Fetal Intestine Small	intestine
26	chr11:73816800-73845400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:73817000-73823000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:73817200-73823600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:73817200-73846800	Weak transcription	Spleen	Spleen
30	chr11:73817400-73823600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:73817400-73823600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:73817400-73823600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:73817400-73823600	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:73817400-73823600	Weak transcription	Fetal Brain Female	brain
35	chr11:73817400-73823600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:73817400-73823800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr11:73817400-73823800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:73817400-73823800	Weak transcription	Ovary	ovary
39	chr11:73817400-73823800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr11:73817400-73823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:73817400-73823800	Weak transcription	K562	blood
42	chr11:73817400-73824000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:73817400-73824000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:73817400-73826800	Weak transcription	Small Intestine	intestine
45	chr11:73817400-73828600	Weak transcription	Right Ventricle	heart
46	chr11:73817400-73845400	Weak transcription	NHDF-Ad	bronchial
47	chr11:73817400-73846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:73817600-73822600	Weak transcription	HUVEC	blood vessel
49	chr11:73817600-73823200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:73817600-73823400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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