Variant report

Variant	rs1203405
Chromosome Location	chr10:52198729-52198730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52193457..52195166-chr10:52196882..52200363,3	K562	blood:
2	chr10:52185055..52188816-chr10:52196257..52198755,3	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1203375	0.90[ASN][1000 genomes]
rs1203382	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203390	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203393	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203394	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203395	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203401	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203403	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203409	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203410	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203411	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203418	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203420	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203421	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1740761	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1810576	0.93[ASN][1000 genomes]
rs1916567	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2221	0.86[ASN][1000 genomes]
rs2339402	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2574985	0.92[ASN][1000 genomes]
rs2983347	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2983350	0.82[ASN][1000 genomes]
rs2983354	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2983357	0.83[ASN][1000 genomes]
rs2983359	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2983361	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2983368	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983369	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983370	0.84[ASN][1000 genomes]
rs2983371	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011770	0.82[AMR][1000 genomes]
rs3011771	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011773	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011779	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011780	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011782	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011783	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011786	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3011787	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011788	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011789	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011790	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3011791	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011792	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011793	0.83[ASN][1000 genomes]
rs3011794	0.83[ASN][1000 genomes]
rs3011797	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3011801	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7912351	0.83[ASN][1000 genomes]
rs920136	0.92[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	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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
9	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
10	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
12	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
13	chr10:52191400-52200400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
18	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
19	chr10:52192400-52199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:52192400-52199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:52192400-52200800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:52192400-52202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:52192400-52219400	Weak transcription	Liver	Liver
25	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
29	chr10:52192400-52230400	Weak transcription	HSMM	muscle
30	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr10:52193400-52205400	Weak transcription	Primary B cells from cord blood	blood
32	chr10:52193400-52206200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:52196200-52198800	Strong transcription	Primary T cells from cord blood	blood
35	chr10:52196400-52198800	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr10:52196800-52199200	Enhancers	Brain Anterior Caudate	brain
37	chr10:52197000-52199200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr10:52197000-52199600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr10:52197000-52200800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr10:52197200-52198800	Enhancers	GM12878-XiMat	blood
41	chr10:52197600-52198800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr10:52197600-52207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:52197800-52199600	Weak transcription	HSMMtube	muscle
44	chr10:52197800-52200000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr10:52197800-52229800	Weak transcription	Gastric	stomach
46	chr10:52198000-52199000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:52198000-52199600	Enhancers	Fetal Thymus	thymus
48	chr10:52198000-52200600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr10:52198200-52207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:52198400-52207400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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