Variant report

Variant	rs11006054
Chromosome Location	chr10:52291770-52291771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52089314..52090958-chr10:52289108..52291926,2	K562	blood:
2	chr10:52273248..52274821-chr10:52291297..52292939,2	MCF-7	breast:
3	chr10:52288714..52294578-chr10:52381112..52386074,5	K562	blood:

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10458673	0.80[AMR][1000 genomes]
rs10508927	1.00[YRI][hapmap]
rs10763382	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10763426	0.82[AMR][1000 genomes]
rs10763535	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10825882	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10825904	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10825934	0.83[AMR][1000 genomes]
rs10825978	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs10826033	0.91[AMR][1000 genomes]
rs10826036	0.91[AMR][1000 genomes]
rs10826161	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10826166	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10826169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10826170	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11005241	1.00[YRI][hapmap]
rs11005262	1.00[YRI][hapmap]
rs11005278	1.00[YRI][hapmap]
rs11005356	1.00[YRI][hapmap]
rs11005418	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs11005579	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs11005614	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs11005621	0.81[AMR][1000 genomes]
rs11006075	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11006084	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11006114	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11006118	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12217518	1.00[YRI][hapmap]
rs12217648	0.80[AMR][1000 genomes]
rs12219070	0.80[AMR][1000 genomes]
rs12219692	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12415817	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12415836	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1884572	0.81[AMR][1000 genomes]
rs1916572	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2024872	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2144861	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3001883	1.00[YRI][hapmap]
rs34122137	0.83[AMR][1000 genomes]
rs34659292	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36122110	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3739989	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4935173	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4935174	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4935728	0.94[AMR][1000 genomes]
rs6481461	1.00[YRI][hapmap]
rs7067552	1.00[YRI][hapmap]
rs7086029	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7089882	1.00[YRI][hapmap]
rs7094143	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7096171	1.00[YRI][hapmap]
rs7907260	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7920818	0.81[AMR][1000 genomes]
rs927048	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs9919413	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
2	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
3	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:52279400-52298200	Weak transcription	Fetal Intestine Small	intestine
7	chr10:52279600-52298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:52279600-52298400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr10:52279600-52298800	Weak transcription	Lung	lung
10	chr10:52279800-52298600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:52282800-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:52283000-52300400	Weak transcription	Psoas Muscle	Psoas
14	chr10:52284400-52292400	Weak transcription	Brain Angular Gyrus	brain
15	chr10:52284600-52297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:52285400-52293200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:52287400-52298200	Weak transcription	Left Ventricle	heart
19	chr10:52287600-52292000	Weak transcription	Stomach Mucosa	stomach
20	chr10:52287600-52294000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:52287600-52296800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr10:52287600-52296800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr10:52287800-52302800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:52288200-52298600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr10:52288600-52300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:52288800-52291800	Weak transcription	Fetal Heart	heart
27	chr10:52289400-52300000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:52290000-52294400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr10:52290000-52295800	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:52290000-52296000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr10:52290000-52296600	Weak transcription	Brain Anterior Caudate	brain
32	chr10:52290200-52296600	Weak transcription	Brain Substantia Nigra	brain
33	chr10:52291200-52292000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr10:52291200-52292800	Enhancers	K562	blood
35	chr10:52291400-52291800	Enhancers	Gastric	stomach
36	chr10:52291600-52293400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr10:52291600-52298600	Weak transcription	Pancreas	Pancrea

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