Variant report

Variant	rs3011780
Chromosome Location	chr10:52287792-52287793
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52285750..52287890-chr10:52311522..52314222,2	MCF-7	breast:
2	chr10:52287492..52289090-chr10:52346967..52349226,2	K562	blood:
3	chr10:52287244..52289297-chr10:52294304..52296791,2	K562	blood:
4	chr10:52120816..52123329-chr10:52287278..52290056,2	MCF-7	breast:
5	chr10:52285770..52288647-chr10:52382026..52387043,4	K562	blood:
6	chr10:52282243..52284789-chr10:52286027..52288655,2	K562	blood:
7	chr10:52285415..52288403-chr10:52289940..52291590,2	K562	blood:
8	chr10:52177517..52180789-chr10:52285364..52288556,3	K562	blood:
9	chr10:52279739..52282600-chr10:52286239..52288790,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11006166	0.86[ASN][1000 genomes]
rs11006179	0.86[ASN][1000 genomes]
rs1203382	0.91[ASN][1000 genomes]
rs1203386	0.91[ASN][1000 genomes]
rs1203390	0.88[ASN][1000 genomes]
rs1203393	0.91[ASN][1000 genomes]
rs1203394	0.88[ASN][1000 genomes]
rs1203395	0.88[ASN][1000 genomes]
rs1203401	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1203403	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203405	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203407	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203409	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203410	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203411	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1203418	0.85[ASN][1000 genomes]
rs1203420	0.85[ASN][1000 genomes]
rs1203421	0.85[ASN][1000 genomes]
rs1740761	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1810576	0.91[ASN][1000 genomes]
rs1916567	0.83[ASN][1000 genomes]
rs2221	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2339402	0.83[ASN][1000 genomes]
rs2574985	0.80[ASN][1000 genomes]
rs2983347	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2983350	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2983354	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983357	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983359	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983361	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983368	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2983369	0.93[ASN][1000 genomes]
rs2983370	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2983371	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3011770	0.85[AMR][1000 genomes]
rs3011771	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3011773	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3011779	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011782	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011786	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3011787	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3011788	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011789	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011790	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3011791	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011792	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011793	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011794	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011797	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3011801	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs920136	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	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
11	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:52 , 50 per page) page: 1 2

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	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
4	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:52273600-52289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:52274800-52288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr10:52279400-52298200	Weak transcription	Fetal Intestine Small	intestine
11	chr10:52279600-52290000	Weak transcription	Primary B cells from cord blood	blood
12	chr10:52279600-52298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:52279600-52298400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr10:52279600-52298800	Weak transcription	Lung	lung
15	chr10:52279800-52298600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:52282800-52291200	Weak transcription	Esophagus	oesophagus
18	chr10:52282800-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:52283000-52300400	Weak transcription	Psoas Muscle	Psoas
20	chr10:52283600-52288200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr10:52283800-52288600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:52284400-52292400	Weak transcription	Brain Angular Gyrus	brain
23	chr10:52284600-52297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:52284800-52289600	Weak transcription	Fetal Lung	lung
25	chr10:52285400-52293200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr10:52285600-52288400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:52286000-52288800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr10:52286200-52288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:52286200-52289400	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:52286200-52291400	Weak transcription	Gastric	stomach
31	chr10:52286400-52288000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:52286800-52288800	Enhancers	Fetal Heart	heart
34	chr10:52287000-52288200	Enhancers	Primary T cells from cord blood	blood
35	chr10:52287000-52288200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr10:52287000-52290200	Enhancers	Brain Substantia Nigra	brain
37	chr10:52287200-52287800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:52287200-52287800	Enhancers	Primary hematopoietic stem cells	blood
39	chr10:52287200-52287800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:52287200-52290000	Enhancers	Brain Cingulate Gyrus	brain
41	chr10:52287400-52287800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr10:52287400-52288400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr10:52287400-52290000	Weak transcription	Right Atrium	heart
44	chr10:52287400-52298200	Weak transcription	Left Ventricle	heart
45	chr10:52287600-52288800	Enhancers	K562	blood
46	chr10:52287600-52289600	Weak transcription	Brain Anterior Caudate	brain
47	chr10:52287600-52291200	Weak transcription	Pancreas	Pancrea
48	chr10:52287600-52291600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr10:52287600-52292000	Weak transcription	Stomach Mucosa	stomach
50	chr10:52287600-52294000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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