Variant report

Variant	rs412056
Chromosome Location	chr5:14807020-14807021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1620976	0.83[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1679138	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs174018	0.83[ASN][1000 genomes]
rs1812659	0.83[EUR][1000 genomes]
rs2448493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453320	0.94[ASN][1000 genomes]
rs258220	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258232	0.94[ASN][1000 genomes]
rs25946	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs26304	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26305	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs26306	0.88[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27353	0.88[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30613	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs31907	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31910	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31911	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31917	0.82[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs31931	0.83[ASN][1000 genomes]
rs31987	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31988	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31989	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31990	0.87[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379016	0.88[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs39917	0.80[ASN][1000 genomes]
rs40402	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42274	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs43178	0.86[ASN][1000 genomes]
rs826351	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826355	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826356	0.83[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826358	0.86[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs879253	0.81[GIH][hapmap]

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
rs412056	ANKH	cis	parietal	SCAN

Chromatin state (count:79 , 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	chr5:14777200-14810400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:14777200-14811400	Weak transcription	Colonic Mucosa	Colon
5	chr5:14778200-14809400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:14778200-14817200	Weak transcription	Fetal Brain Female	brain
7	chr5:14785800-14809600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:14788400-14809600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:14788600-14809600	Weak transcription	Psoas Muscle	Psoas
10	chr5:14788800-14809600	Weak transcription	Liver	Liver
11	chr5:14790600-14809800	Weak transcription	Stomach Mucosa	stomach
12	chr5:14791000-14809600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:14791400-14809800	Weak transcription	Aorta	Aorta
14	chr5:14791600-14809600	Weak transcription	Fetal Intestine Large	intestine
15	chr5:14791600-14809600	Weak transcription	Small Intestine	intestine
16	chr5:14793800-14810000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:14795200-14809400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:14795400-14809600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:14795400-14809600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:14795600-14809600	Weak transcription	Brain Anterior Caudate	brain
22	chr5:14796400-14821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:14798200-14809600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:14799600-14809600	Weak transcription	HSMMtube	muscle
25	chr5:14801200-14811200	Weak transcription	Esophagus	oesophagus
26	chr5:14802400-14809600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:14802400-14809800	Weak transcription	Primary T cells from cord blood	blood
28	chr5:14802600-14809400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr5:14802600-14809600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:14802600-14809600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:14802800-14809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:14802800-14809600	Weak transcription	Lung	lung
33	chr5:14803000-14809400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:14803000-14809600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:14803000-14809600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:14803000-14809600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:14803000-14809600	Weak transcription	Spleen	Spleen
38	chr5:14803000-14809600	Weak transcription	A549	lung
39	chr5:14803200-14809600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:14803200-14810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:14804000-14808000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:14805000-14810000	Weak transcription	Pancreas	Pancrea
43	chr5:14805200-14809600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:14805600-14807800	Enhancers	Right Ventricle	heart
45	chr5:14805800-14807200	Enhancers	Brain Substantia Nigra	brain
46	chr5:14805800-14807400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:14805800-14807400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:14805800-14807600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:14805800-14807600	Enhancers	Left Ventricle	heart
50	chr5:14805800-14807800	Enhancers	Brain Hippocampus Middle	brain

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