Variant report

Variant	rs1550826
Chromosome Location	chr5:14840668-14840669
allele	A/G
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:32)

rs_ID	r²[population]
rs1004673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175317	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1374080	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1620976	0.85[MKK][hapmap]
rs166298	0.82[EUR][1000 genomes]
rs17251715	0.87[CEU][hapmap]
rs17251763	0.89[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs17266101	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17317514	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs17318936	0.99[ASN][1000 genomes]
rs2401985	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs258221	0.83[CHB][hapmap];0.89[ASN][1000 genomes]
rs258223	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs26306	0.83[MKK][hapmap]
rs27353	0.84[MKK][hapmap]
rs31908	0.86[ASN][1000 genomes]
rs31916	0.89[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs31918	0.98[ASN][1000 genomes]
rs33101	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35554212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35842463	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368503	0.89[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs398961	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs40970	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs4569871	0.89[ASN][1000 genomes]
rs4702056	0.98[ASN][1000 genomes]
rs55954907	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61169618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61394862	0.98[ASN][1000 genomes]
rs6884206	0.91[ASN][1000 genomes]
rs7715323	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs826356	0.88[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	esv2753381	chr5:14814900-14882800	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	esv2755533	chr5:14814900-14882800	Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	esv2755538	chr5:14814900-14927500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1550826	ANKH	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14811600-14843800	Weak transcription	Fetal Intestine Large	intestine
2	chr5:14811600-14861200	Weak transcription	Colonic Mucosa	Colon
3	chr5:14812000-14849600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:14814400-14842200	Weak transcription	Thymus	Thymus
5	chr5:14817400-14842400	Weak transcription	Lung	lung
6	chr5:14820600-14854800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:14820800-14851800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:14821200-14848600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:14824800-14869600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:14826600-14841800	Weak transcription	HepG2	liver
11	chr5:14827600-14850000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:14827800-14854600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:14828000-14843800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:14828600-14846600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr5:14828800-14856200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:14830400-14852200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:14830400-14866400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:14831000-14870400	Weak transcription	Spleen	Spleen
19	chr5:14831200-14848800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:14831600-14845400	Weak transcription	Fetal Intestine Small	intestine
21	chr5:14831600-14849600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:14833200-14846800	Weak transcription	Liver	Liver
23	chr5:14833800-14849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:14834200-14842400	Weak transcription	Brain Angular Gyrus	brain
25	chr5:14834200-14844400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:14834200-14849800	Weak transcription	Right Ventricle	heart
27	chr5:14834400-14842400	Weak transcription	Psoas Muscle	Psoas
28	chr5:14835600-14850000	Weak transcription	Gastric	stomach
29	chr5:14835600-14869000	Weak transcription	NHDF-Ad	bronchial
30	chr5:14835800-14840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:14835800-14842800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:14835800-14844400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:14835800-14844400	Weak transcription	Brain Substantia Nigra	brain
34	chr5:14835800-14845400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:14835800-14849600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:14835800-14849600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:14835800-14850800	Weak transcription	Brain Anterior Caudate	brain
38	chr5:14835800-14851400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:14835800-14864200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:14837000-14849600	Weak transcription	Hela-S3	cervix
41	chr5:14837400-14869400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:14837800-14848800	Weak transcription	NHEK	skin
43	chr5:14838000-14842800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:14838200-14848600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr5:14838200-14852200	Weak transcription	Small Intestine	intestine
46	chr5:14838600-14849800	Strong transcription	Osteobl	bone
47	chr5:14838800-14848800	Weak transcription	Fetal Brain Female	brain
48	chr5:14839000-14844400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:14839000-14845400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:14839200-14842400	Weak transcription	Left Ventricle	heart

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