Variant report

Variant	rs258227
Chromosome Location	chr5:14802111-14802112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1061813	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11133799	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1117282	0.83[ASN][1000 genomes]
rs12653321	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13155894	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1353258	0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1812658	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2453316	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs258218	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs258219	0.93[CHB][hapmap];0.98[ASN][1000 genomes]
rs258222	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258224	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258225	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258226	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258228	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258231	0.93[CHB][hapmap];0.98[ASN][1000 genomes]
rs25957	0.92[CHB][hapmap];0.95[ASN][1000 genomes]
rs28005	0.96[ASN][1000 genomes]
rs28006	0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[ASN][1000 genomes]
rs28108	0.98[ASN][1000 genomes]
rs30615	0.89[ASN][1000 genomes]
rs31909	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs31912	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31933	0.93[CHB][hapmap];0.98[ASN][1000 genomes]
rs31990	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs33102	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39636	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs39916	0.93[ASN][1000 genomes]
rs42679	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42680	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs573116	0.87[ASN][1000 genomes]
rs826352	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826357	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs879253	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9790982	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][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	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830212	chr5:14784197-14966683	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs258227	ANKH	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14767400-14809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:14776800-14809400	Weak transcription	HMEC	breast
3	chr5:14777200-14806200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:14777200-14810400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:14777200-14811400	Weak transcription	Colonic Mucosa	Colon
6	chr5:14778200-14805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:14778200-14809400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:14778200-14817200	Weak transcription	Fetal Brain Female	brain
9	chr5:14782200-14805800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:14784800-14806600	Weak transcription	Adipose Nuclei	Adipose
11	chr5:14785800-14809600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:14788400-14809600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:14788600-14809600	Weak transcription	Psoas Muscle	Psoas
14	chr5:14788800-14809600	Weak transcription	Liver	Liver
15	chr5:14790600-14809800	Weak transcription	Stomach Mucosa	stomach
16	chr5:14791000-14806000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:14791000-14809600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:14791400-14809800	Weak transcription	Aorta	Aorta
19	chr5:14791600-14802800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:14791600-14809600	Weak transcription	Fetal Intestine Large	intestine
21	chr5:14791600-14809600	Weak transcription	Small Intestine	intestine
22	chr5:14793800-14804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:14793800-14810000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:14794400-14802200	Weak transcription	Right Ventricle	heart
25	chr5:14794400-14805800	Weak transcription	HepG2	liver
26	chr5:14794600-14806600	Weak transcription	Gastric	stomach
27	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:14795400-14805800	Weak transcription	Fetal Heart	heart
30	chr5:14795400-14809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:14795400-14809600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:14795600-14809600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:14795800-14804400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:14796000-14802600	Weak transcription	Fetal Intestine Small	intestine
35	chr5:14796400-14804600	Weak transcription	Hela-S3	cervix
36	chr5:14796400-14821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:14798000-14805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:14798000-14805800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:14798000-14805800	Weak transcription	Brain Substantia Nigra	brain
40	chr5:14798000-14805800	Weak transcription	NHDF-Ad	bronchial
41	chr5:14798200-14805800	Weak transcription	Brain Angular Gyrus	brain
42	chr5:14798200-14809600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr5:14799000-14805800	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:14799600-14809600	Weak transcription	HSMMtube	muscle
45	chr5:14799800-14804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:14800000-14803000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr5:14800400-14803400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr5:14801000-14806000	Strong transcription	Osteobl	bone
49	chr5:14801200-14802200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr5:14801200-14811200	Weak transcription	Esophagus	oesophagus

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