Variant report

Variant	rs25860
Chromosome Location	chr5:53474256-53474257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10052279	1.00[CHB][hapmap]
rs10055804	1.00[CHB][hapmap]
rs10057147	1.00[CHB][hapmap]
rs10065324	1.00[CHB][hapmap]
rs10079659	1.00[CHB][hapmap]
rs11748223	1.00[JPT][hapmap]
rs11953312	1.00[CHB][hapmap]
rs13358454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435967	1.00[CHB][hapmap]
rs1423609	1.00[JPT][hapmap]
rs154022	0.82[YRI][hapmap]
rs156696	1.00[CHB][hapmap]
rs156832	1.00[CHB][hapmap]
rs157235	1.00[CHB][hapmap]
rs1645549	1.00[CHB][hapmap]
rs1664668	1.00[CHB][hapmap]
rs16882296	1.00[CHB][hapmap]
rs16882383	1.00[CHB][hapmap]
rs16882423	1.00[CHB][hapmap]
rs16882424	1.00[CHB][hapmap]
rs16882437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16882447	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267677	1.00[JPT][hapmap]
rs181916	1.00[ASN][1000 genomes]
rs255678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs25854	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs25861	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27664	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27677	1.00[CHB][hapmap]
rs277335	1.00[JPT][hapmap]
rs277336	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277339	1.00[JPT][hapmap]
rs277340	1.00[JPT][hapmap]
rs277341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277342	1.00[JPT][hapmap]
rs2783	1.00[CHB][hapmap]
rs3797247	1.00[CHB][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs3797252	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846490	1.00[CHB][hapmap]
rs4373242	1.00[CHB][hapmap]
rs57562307	0.85[EUR][1000 genomes]
rs59430615	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674377	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871446	1.00[CHB][hapmap]
rs6879693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6896006	1.00[CHB][hapmap]
rs7705101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713087	1.00[CHB][hapmap]
rs7715885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9292039	1.00[CHB][hapmap]
rs9292040	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
20	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs25860	ANKRD55	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53433000-53480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:53451400-53476200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:53456000-53483000	Weak transcription	Right Ventricle	heart
4	chr5:53461800-53475000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:53463400-53476200	Weak transcription	NHDF-Ad	bronchial
6	chr5:53466400-53476600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:53466400-53484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:53466800-53489000	Weak transcription	K562	blood
9	chr5:53467200-53483200	Weak transcription	Primary T cells from cord blood	blood
10	chr5:53467800-53475000	Weak transcription	Pancreas	Pancrea
11	chr5:53469800-53482000	Weak transcription	Psoas Muscle	Psoas
12	chr5:53470800-53474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:53471800-53476800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:53472000-53474600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:53472200-53474400	Enhancers	Brain Cingulate Gyrus	brain
16	chr5:53472600-53474400	Enhancers	Small Intestine	intestine
17	chr5:53472600-53475000	Weak transcription	Gastric	stomach
18	chr5:53472600-53475600	Enhancers	Fetal Intestine Large	intestine
19	chr5:53472800-53475200	Enhancers	Stomach Mucosa	stomach
20	chr5:53472800-53475400	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr5:53472800-53475600	Enhancers	Fetal Intestine Small	intestine
22	chr5:53472800-53476200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:53473000-53476000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:53473000-53476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:53473200-53475400	Enhancers	Fetal Lung	lung
26	chr5:53473200-53475600	Enhancers	Colon Smooth Muscle	Colon
27	chr5:53473400-53475200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr5:53473600-53475600	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:53473800-53474600	Enhancers	Left Ventricle	heart
30	chr5:53473800-53476200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:53474000-53474400	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr5:53474000-53475000	Weak transcription	Right Atrium	heart
33	chr5:53474000-53476200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:53474000-53481600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr5:53474200-53474400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr5:53474200-53474400	Enhancers	Brain Hippocampus Middle	brain
37	chr5:53474200-53474600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:53474200-53474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:53474200-53475000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:53474200-53476600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:53474200-53490800	Weak transcription	Rectal Smooth Muscle	rectum

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