Variant report

Variant	rs9562886
Chromosome Location	chr13:50077446-50077447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50069004..50071273-chr13:50075738..50077658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11148145	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57318076	0.84[AMR][1000 genomes]
rs9562889	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568212	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
2	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
3	chr13:50070800-50086800	Weak transcription	Ovary	ovary
4	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
5	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
7	chr13:50070800-50087800	Weak transcription	NHEK	skin
8	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
10	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
11	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
14	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
15	chr13:50071000-50077800	Weak transcription	Fetal Intestine Small	intestine
16	chr13:50071000-50078200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:50071000-50079800	Weak transcription	Brain Hippocampus Middle	brain
18	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
19	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
21	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr13:50071000-50093400	Weak transcription	HepG2	liver
23	chr13:50071200-50081600	Weak transcription	Thymus	Thymus
24	chr13:50071400-50081600	Weak transcription	Fetal Muscle Leg	muscle
25	chr13:50071400-50087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:50071400-50087200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:50071600-50078400	Strong transcription	Fetal Thymus	thymus
28	chr13:50071800-50087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr13:50071800-50088000	Weak transcription	Pancreas	Pancrea
30	chr13:50072000-50078400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr13:50072600-50078000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr13:50073200-50078400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr13:50073800-50081600	Weak transcription	Liver	Liver
34	chr13:50074000-50093000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr13:50074400-50077600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:50074600-50081400	Weak transcription	Dnd41	blood
37	chr13:50074800-50079400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr13:50074800-50079400	Weak transcription	HSMMtube	muscle
39	chr13:50074800-50086400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:50075000-50079400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:50075000-50079400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:50075000-50079400	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr13:50075000-50079400	Weak transcription	HSMM	muscle
44	chr13:50075000-50080800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:50075000-50086800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:50075000-50087000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:50075000-50087800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr13:50075000-50087800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr13:50075000-50088200	Weak transcription	HMEC	breast
50	chr13:50075000-50102400	Weak transcription	NH-A	brain

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