Variant report

Variant	rs2339401
Chromosome Location	chr10:52141771-52141772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52140574..52146052-chr10:52147232..52152526,7	K562	blood:
2	chr10:52139930..52141788-chr10:52152560..52154138,2	MCF-7	breast:
3	chr10:52140515..52144174-chr10:52145469..52147444,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269700	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10508927	0.88[JPT][hapmap]
rs10508928	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10508929	0.84[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10733968	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10740684	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10763373	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10763382	0.88[JPT][hapmap]
rs10763392	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10763500	0.84[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs10825789	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10825825	0.99[ASN][1000 genomes]
rs10825859	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10825861	0.88[JPT][hapmap]
rs10825882	0.88[JPT][hapmap]
rs10825904	0.84[JPT][hapmap]
rs10825978	0.88[JPT][hapmap]
rs10825995	0.83[CEU][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs10825996	0.82[CEU][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs10826013	0.84[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs10826034	0.80[ASN][1000 genomes]
rs11005356	0.84[JPT][hapmap]
rs11005399	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11005415	0.99[ASN][1000 genomes]
rs11005418	0.84[JPT][hapmap]
rs11005579	0.86[JPT][hapmap]
rs11005614	0.88[JPT][hapmap]
rs11005761	0.81[EUR][1000 genomes]
rs1916572	0.84[JPT][hapmap]
rs2273402	0.84[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2339400	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339507	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs3739989	0.88[JPT][hapmap]
rs4935165	0.81[EUR][1000 genomes]
rs4935711	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7074024	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086029	0.82[JPT][hapmap]
rs7090807	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7092749	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7093878	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094029	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768185	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7896315	0.84[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7920818	0.82[JPT][hapmap]
rs7922802	0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs910817	0.80[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs927047	0.81[CEU][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv430231	chr10:52119046-52163531	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52104200-52157000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52115800-52142200	Weak transcription	Fetal Intestine Small	intestine
3	chr10:52133200-52142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:52133600-52146800	Weak transcription	Stomach Mucosa	stomach
5	chr10:52134600-52146400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr10:52134800-52145000	Weak transcription	HSMMtube	muscle
7	chr10:52135400-52142200	Weak transcription	Small Intestine	intestine
8	chr10:52135400-52142400	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:52135400-52154000	Weak transcription	Right Ventricle	heart
10	chr10:52135600-52143600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr10:52135600-52152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:52135800-52144200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr10:52135800-52145400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:52135800-52155400	Weak transcription	Primary T cells from cord blood	blood
15	chr10:52136000-52144600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:52136000-52155400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr10:52136200-52142600	Weak transcription	A549	lung
18	chr10:52136800-52152600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:52137000-52154800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:52137600-52143000	Enhancers	Brain Substantia Nigra	brain
21	chr10:52137800-52143000	Enhancers	Fetal Lung	lung
22	chr10:52137800-52145600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:52137800-52153600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:52138200-52146200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr10:52138400-52148000	Enhancers	Brain Hippocampus Middle	brain
26	chr10:52139000-52142800	Enhancers	Brain Cingulate Gyrus	brain
27	chr10:52139200-52143000	Enhancers	Brain Anterior Caudate	brain
28	chr10:52139600-52142400	Enhancers	Left Ventricle	heart
29	chr10:52139600-52145800	Enhancers	Adipose Nuclei	Adipose
30	chr10:52139800-52142400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:52139800-52145200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr10:52139800-52145400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:52139800-52146800	Weak transcription	Primary B cells from cord blood	blood
34	chr10:52140000-52145400	Weak transcription	Lung	lung
35	chr10:52140000-52154600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:52140200-52142000	Enhancers	Right Atrium	heart
37	chr10:52140400-52143000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr10:52140400-52143600	Weak transcription	Ovary	ovary
39	chr10:52140400-52143600	Weak transcription	K562	blood
40	chr10:52140400-52144600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr10:52140400-52156800	Weak transcription	Gastric	stomach
42	chr10:52140400-52157000	Weak transcription	Aorta	Aorta
43	chr10:52140600-52144200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:52140600-52144200	Weak transcription	Brain Angular Gyrus	brain
45	chr10:52140600-52147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr10:52141000-52143000	Enhancers	NHDF-Ad	bronchial
47	chr10:52141000-52144000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:52141000-52144400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:52141200-52142000	Weak transcription	GM12878-XiMat	blood
50	chr10:52141200-52142800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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