Variant report

Variant	rs826062
Chromosome Location	chr11:73787381-73787382
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73780196..73782552-chr11:73785196..73788423,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168014	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10898954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10898956	0.80[ASN][1000 genomes]
rs1614299	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615115	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1685355	0.86[JPT][hapmap]
rs1726735	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1726744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1726745	0.87[JPT][hapmap]
rs1726746	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1726751	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs1726752	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1726764	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs1783537	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1790381	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1790404	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]
rs2007567	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2075577	0.87[JPT][hapmap]
rs3018184	0.83[EUR][1000 genomes]
rs4453265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs474835	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4944036	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944038	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944878	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500608	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs575096	0.88[EUR][1000 genomes]
rs588097	0.87[JPT][hapmap]
rs590336	0.87[JPT][hapmap]
rs635441	0.87[JPT][hapmap]
rs647126	0.87[JPT][hapmap]
rs6592545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592551	0.80[EUR][1000 genomes]
rs7121868	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7483884	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7926165	0.87[JPT][hapmap]
rs826033	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs826039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs826056	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826066	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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
rs826062	FGF19	cis	cerebellum	SCAN
rs826062	P4HA3	cis	Thyroid	GTEx
rs826062	C2CD3	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73730800-73800800	Weak transcription	Fetal Heart	heart
2	chr11:73750800-73800400	Weak transcription	HMEC	breast
3	chr11:73753200-73796400	Weak transcription	Small Intestine	intestine
4	chr11:73753200-73804600	Weak transcription	Colonic Mucosa	Colon
5	chr11:73760000-73802600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:73768800-73798200	Weak transcription	NHEK	skin
7	chr11:73769000-73788600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:73771200-73789000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:73777000-73788400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:73777600-73788600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:73778000-73790600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:73778200-73789800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:73778200-73791000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:73778400-73790000	Strong transcription	Fetal Thymus	thymus
16	chr11:73778800-73790200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:73778800-73790400	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:73778800-73790400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr11:73778800-73792800	Strong transcription	Primary B cells from cord blood	blood
20	chr11:73779000-73790200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:73779000-73792600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr11:73779200-73791000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:73779600-73790800	Strong transcription	Primary T cells from cord blood	blood
24	chr11:73779800-73789000	Weak transcription	HepG2	liver
25	chr11:73780200-73790400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:73780200-73790800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:73780600-73790000	Strong transcription	Hela-S3	cervix
28	chr11:73780600-73790400	Strong transcription	Dnd41	blood
29	chr11:73781200-73795800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:73781400-73790200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
32	chr11:73782200-73796400	Weak transcription	Right Ventricle	heart
33	chr11:73782600-73789000	Weak transcription	Pancreas	Pancrea
34	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr11:73782800-73790400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:73782800-73790600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr11:73782800-73795400	Weak transcription	K562	blood
38	chr11:73783200-73789800	Strong transcription	Adipose Nuclei	Adipose
39	chr11:73783400-73789800	Strong transcription	Brain Angular Gyrus	brain
40	chr11:73783600-73790400	Strong transcription	Placenta	Placenta
41	chr11:73784200-73796600	Weak transcription	Psoas Muscle	Psoas
42	chr11:73784200-73801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:73785000-73789000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:73785400-73788200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:73785400-73788800	Weak transcription	Fetal Brain Male	brain
46	chr11:73785400-73789000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:73785400-73789000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:73785400-73789000	Weak transcription	Fetal Lung	lung
49	chr11:73785400-73789000	Weak transcription	A549	lung
50	chr11:73785400-73789200	Weak transcription	Osteobl	bone

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