Variant report

Variant	rs2453
Chromosome Location	chr10:6469673-6469674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10906490	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10906569	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11258536	0.88[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap]
rs11258608	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11258610	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11258759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11258762	0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11258959	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11258960	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11816284	0.94[CEU][hapmap];0.84[JPT][hapmap]
rs12146312	0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs12358161	1.00[LWK][hapmap]
rs4364968	0.92[CHD][hapmap]
rs4750434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4750439	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4750457	0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs4750461	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4750495	1.00[ASW][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs586457	0.86[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs670804	0.86[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs673964	0.86[CHD][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs677986	0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs681803	0.80[EUR][1000 genomes]
rs7076533	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7091849	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7095942	1.00[LWK][hapmap]
rs7096751	1.00[LWK][hapmap]
rs7099451	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.85[EUR][1000 genomes]
rs72781706	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7918373	1.00[ASW][hapmap];1.00[CHD][hapmap]
rs7920048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs943456	0.85[EUR][1000 genomes]
rs944712	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944713	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs944715	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1053177	chr10:6453307-6473114	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2453	ANKRD16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6452600-6478600	Weak transcription	Brain Anterior Caudate	brain
2	chr10:6452600-6481400	Weak transcription	Brain Substantia Nigra	brain
3	chr10:6453200-6470800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr10:6454000-6472800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:6456200-6496600	Weak transcription	Pancreas	Pancrea
6	chr10:6459800-6472600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr10:6460600-6481200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:6460800-6472600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:6464200-6487200	Strong transcription	Fetal Thymus	thymus
10	chr10:6464400-6485800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:6464600-6490600	Strong transcription	Primary T cells from cord blood	blood
12	chr10:6464800-6487400	Strong transcription	Thymus	Thymus
13	chr10:6465800-6481000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:6465800-6486600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr10:6465800-6496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:6465800-6496600	Weak transcription	Psoas Muscle	Psoas
17	chr10:6465800-6501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:6466000-6475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr10:6466000-6486600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:6466200-6469800	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:6466400-6487800	Weak transcription	Fetal Stomach	stomach
22	chr10:6467000-6487200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr10:6467400-6496200	Weak transcription	Lung	lung
24	chr10:6467600-6481000	Weak transcription	Fetal Intestine Small	intestine
25	chr10:6467600-6487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:6467800-6471400	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr10:6467800-6473600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr10:6467800-6486000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr10:6467800-6487000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:6467800-6487400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:6467800-6487600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr10:6468000-6473800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:6468000-6483800	Weak transcription	K562	blood
34	chr10:6468000-6487600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr10:6468000-6487800	Weak transcription	Brain Angular Gyrus	brain
36	chr10:6468200-6473600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr10:6468200-6496800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr10:6468400-6477600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr10:6468400-6478800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:6468400-6484600	Weak transcription	Spleen	Spleen
41	chr10:6469000-6471200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr10:6469200-6469800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:6469200-6470200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr10:6469200-6470200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr10:6469200-6470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:6469200-6471000	Strong transcription	Fetal Muscle Leg	muscle
47	chr10:6469200-6473400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:6469200-6477400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr10:6469200-6479400	Strong transcription	Dnd41	blood
50	chr10:6469600-6473800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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