Variant report

Variant	rs2339508
Chromosome Location	chr10:52286958-52286959
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52085739..52087419-chr10:52285865..52287749,2	K562	blood:
2	chr10:52285750..52287890-chr10:52311522..52314222,2	MCF-7	breast:
3	chr10:52285770..52287442-chr10:52383427..52386172,2	K562	blood:
4	chr10:52285770..52288647-chr10:52382026..52387043,4	K562	blood:
5	chr10:52282243..52284789-chr10:52286027..52288655,2	K562	blood:
6	chr10:52285415..52288403-chr10:52289940..52291590,2	K562	blood:
7	chr10:52177517..52180789-chr10:52285364..52288556,3	K562	blood:
8	chr10:52279739..52282600-chr10:52286239..52288790,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2208035	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2208037	0.81[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339509	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860490	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983348	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2983352	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983358	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983362	0.86[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983363	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983365	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983372	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3001855	0.81[YRI][hapmap]
rs3011708	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3011778	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011781	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011799	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094723	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[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:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
3	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
4	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
5	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr10:52273400-52287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:52273400-52287200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:52273600-52287400	Weak transcription	GM12878-XiMat	blood
11	chr10:52273600-52289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:52274000-52287200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:52274800-52288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:52279400-52298200	Weak transcription	Fetal Intestine Small	intestine
18	chr10:52279600-52290000	Weak transcription	Primary B cells from cord blood	blood
19	chr10:52279600-52298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:52279600-52298400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:52279600-52298800	Weak transcription	Lung	lung
22	chr10:52279800-52287200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:52279800-52298600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr10:52282800-52291200	Weak transcription	Esophagus	oesophagus
26	chr10:52282800-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:52283000-52300400	Weak transcription	Psoas Muscle	Psoas
28	chr10:52283600-52288200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr10:52283800-52287200	Weak transcription	Right Atrium	heart
30	chr10:52283800-52288600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr10:52284200-52287000	Weak transcription	Primary T cells from cord blood	blood
32	chr10:52284200-52287000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr10:52284400-52292400	Weak transcription	Brain Angular Gyrus	brain
34	chr10:52284600-52287200	Weak transcription	Brain Anterior Caudate	brain
35	chr10:52284600-52287200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:52284600-52287200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr10:52284600-52287400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr10:52284600-52297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:52284800-52289600	Weak transcription	Fetal Lung	lung
40	chr10:52285200-52287000	Weak transcription	Brain Substantia Nigra	brain
41	chr10:52285400-52293200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr10:52285600-52288400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr10:52285800-52287200	Genic enhancers	K562	blood
44	chr10:52286000-52288800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr10:52286200-52288200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr10:52286200-52289400	Weak transcription	Brain Hippocampus Middle	brain
47	chr10:52286200-52291400	Weak transcription	Gastric	stomach
48	chr10:52286400-52287600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:52286400-52288000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr10:52286400-52304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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