Variant report

Variant	rs11590106
Chromosome Location	chr1:95505835-95505836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10465759	0.93[JPT][hapmap]
rs11165297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11801110	0.92[JPT][hapmap]
rs12129041	0.80[JPT][hapmap]
rs12717800	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12751633	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12755096	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12760863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17112857	0.93[JPT][hapmap]
rs2391390	0.93[JPT][hapmap]
rs2391391	0.82[JPT][hapmap]
rs35328371	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3890785	0.93[JPT][hapmap]
rs4131811	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662345	0.93[JPT][hapmap]
rs6669262	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6671842	0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6674467	0.92[JPT][hapmap]
rs6674604	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6678809	0.93[JPT][hapmap]
rs6679106	0.93[JPT][hapmap]
rs6684137	0.93[JPT][hapmap]
rs6687351	0.93[JPT][hapmap]
rs6695561	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6698894	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs71652601	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71652602	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74101985	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540821	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7543156	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9661047	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3402740	chr1:95500980-95527860	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11590106	FNBP1L	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95480000-95508800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:95485200-95507000	Weak transcription	Fetal Heart	heart
3	chr1:95488000-95507000	Weak transcription	Ovary	ovary
4	chr1:95488200-95507000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
6	chr1:95488400-95507000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:95488400-95507800	Weak transcription	Brain Substantia Nigra	brain
8	chr1:95488600-95507800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:95489400-95517200	Weak transcription	Aorta	Aorta
10	chr1:95491400-95507000	Weak transcription	Fetal Kidney	kidney
11	chr1:95491600-95529600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr1:95492600-95507800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:95492800-95507000	Weak transcription	Fetal Stomach	stomach
14	chr1:95492800-95508800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:95493400-95508800	Weak transcription	Liver	Liver
16	chr1:95495200-95508000	Weak transcription	HepG2	liver
17	chr1:95495200-95508800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:95495400-95507000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:95497000-95508000	Weak transcription	Left Ventricle	heart
20	chr1:95500600-95507000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:95501400-95506800	Weak transcription	NHLF	lung
22	chr1:95501800-95506000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:95501800-95506000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:95501800-95506000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:95501800-95506800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:95501800-95507000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:95501800-95507000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:95502000-95507000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:95502000-95512200	Weak transcription	GM12878-XiMat	blood
30	chr1:95502600-95508000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:95502600-95509000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:95504400-95506200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:95504400-95506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:95504400-95507200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:95504400-95507200	Enhancers	NHEK	skin
36	chr1:95504400-95507400	Enhancers	HMEC	breast
37	chr1:95504600-95506200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:95504800-95506200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:95504800-95506800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:95505000-95507800	Enhancers	HSMM	muscle
41	chr1:95505000-95508800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:95505400-95506000	Enhancers	Pancreas	Pancrea
43	chr1:95505400-95506200	Enhancers	Small Intestine	intestine
44	chr1:95505400-95507000	Weak transcription	Osteobl	bone
45	chr1:95505600-95507000	Weak transcription	NH-A	brain
46	chr1:95505600-95537400	Weak transcription	Right Atrium	heart
47	chr1:95505800-95506000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:95505800-95506000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:95505800-95506200	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:95505800-95506200	Enhancers	Placenta	Placenta

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