Variant report

Variant	rs10825934
Chromosome Location	chr10:52173338-52173339
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52160595..52164108-chr10:52172645..52175372,3	MCF-7	breast:
2	chr10:52169460..52174968-chr10:52176430..52182227,8	K562	blood:
3	chr10:52165612..52167461-chr10:52171890..52173400,2	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10458673	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10508927	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10508928	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10508929	0.99[ASN][1000 genomes]
rs10740684	0.99[ASN][1000 genomes]
rs10763365	0.85[EUR][1000 genomes]
rs10763373	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10763382	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10763426	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10763500	0.88[ASN][1000 genomes]
rs10825789	0.84[EUR][1000 genomes]
rs10825825	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10825859	0.93[ASN][1000 genomes]
rs10825861	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10825882	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10825904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825978	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10825995	0.92[ASN][1000 genomes]
rs10825996	0.92[ASN][1000 genomes]
rs10826013	0.92[ASN][1000 genomes]
rs10826033	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10826036	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10826169	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11005356	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11005399	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11005415	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11005418	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11005579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11005614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005621	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11005761	0.90[ASN][1000 genomes]
rs11005803	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11005884	0.88[ASN][1000 genomes]
rs11006054	0.83[AMR][1000 genomes]
rs11006075	0.81[AMR][1000 genomes]
rs12217648	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12219070	0.89[ASN][1000 genomes]
rs12219692	0.90[AFR][1000 genomes]
rs1884572	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1916572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024872	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2144863	0.85[ASN][1000 genomes]
rs2273402	0.86[ASN][1000 genomes]
rs2339503	0.87[ASN][1000 genomes]
rs2339507	0.85[ASN][1000 genomes]
rs34122137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739989	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4519042	0.81[AFR][1000 genomes]
rs4935165	0.88[ASN][1000 genomes]
rs4935711	0.87[ASN][1000 genomes]
rs4935728	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7079881	0.84[ASN][1000 genomes]
rs7086029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7090807	0.88[ASN][1000 genomes]
rs7092749	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs768185	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7896315	0.87[ASN][1000 genomes]
rs7904375	0.86[EUR][1000 genomes]
rs7908163	0.82[EUR][1000 genomes]
rs7920818	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs910817	0.84[ASN][1000 genomes]
rs927047	0.84[ASN][1000 genomes]
rs927048	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][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	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52147000-52176600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:52157200-52177600	Weak transcription	Spleen	Spleen
3	chr10:52157800-52175400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:52157800-52176800	Weak transcription	Lung	lung
5	chr10:52160800-52176800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr10:52163600-52176800	Weak transcription	Thymus	Thymus
7	chr10:52164400-52173800	Weak transcription	Psoas Muscle	Psoas
8	chr10:52164400-52174000	Weak transcription	Brain Angular Gyrus	brain
9	chr10:52164400-52177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:52164600-52176600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:52166600-52175800	Weak transcription	Primary T cells from cord blood	blood
12	chr10:52166600-52177400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr10:52166800-52177200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr10:52166800-52177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:52167000-52176800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:52167000-52176800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr10:52167000-52177200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr10:52167000-52177400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr10:52167600-52176800	Weak transcription	Primary B cells from cord blood	blood
20	chr10:52168000-52177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr10:52168600-52176200	Weak transcription	Right Atrium	heart
22	chr10:52168600-52176600	Weak transcription	Fetal Brain Male	brain
23	chr10:52170000-52174200	Enhancers	Brain Substantia Nigra	brain
24	chr10:52170200-52176400	Weak transcription	Small Intestine	intestine
25	chr10:52170200-52176800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:52170400-52175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:52170400-52175000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:52170400-52175200	Enhancers	Hela-S3	cervix
29	chr10:52170400-52176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:52170400-52176800	Weak transcription	Right Ventricle	heart
31	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
32	chr10:52170600-52174000	Weak transcription	Left Ventricle	heart
33	chr10:52170600-52175200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:52170600-52175200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr10:52170600-52175600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr10:52170600-52176200	Weak transcription	HMEC	breast
37	chr10:52170600-52176600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr10:52170600-52176600	Weak transcription	NH-A	brain
39	chr10:52170600-52176800	Weak transcription	Aorta	Aorta
40	chr10:52170600-52177400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr10:52170600-52177400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr10:52170600-52177600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:52170800-52176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:52171000-52173600	Enhancers	Brain Cingulate Gyrus	brain
45	chr10:52171200-52175000	Weak transcription	NHDF-Ad	bronchial
46	chr10:52171200-52175200	Weak transcription	HSMM	muscle
47	chr10:52171400-52175400	Weak transcription	NHEK	skin
48	chr10:52171400-52175400	Weak transcription	NHLF	lung
49	chr10:52171400-52176000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr10:52171400-52176000	Weak transcription	Muscle Satellite Cultured Cells	--

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