Variant report

Variant	rs9562880
Chromosome Location	chr13:50027846-50027847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50022438..50024030-chr13:50027384..50029296,2	MCF-7	breast:
2	chr13:50027025..50029589-chr13:50038716..50040663,2	MCF-7	breast:
3	chr13:50017298..50020087-chr13:50026645..50030235,3	MCF-7	breast:
4	chr13:50027049..50030534-chr13:50032779..50035441,4	K562	blood:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17381926	0.81[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41284778	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56737298	0.95[ASN][1000 genomes]
rs59837207	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66771344	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67714799	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7317398	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73188659	0.88[EUR][1000 genomes]
rs73190705	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7331182	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8000963	0.82[JPT][hapmap]
rs9562881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562888	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568205	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568227	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568231	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568240	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	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
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	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
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	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
11	esv1807924	chr13:49991885-50036730	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1796315	chr13:49992988-50031868	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50019400-50036200	Weak transcription	Esophagus	oesophagus
2	chr13:50019600-50028200	Weak transcription	Fetal Stomach	stomach
3	chr13:50019600-50028600	Weak transcription	Fetal Lung	lung
4	chr13:50019600-50034400	Weak transcription	Adipose Nuclei	Adipose
5	chr13:50019600-50035400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:50019600-50035400	Weak transcription	Brain Substantia Nigra	brain
7	chr13:50019600-50035800	Weak transcription	Left Ventricle	heart
8	chr13:50019600-50035800	Weak transcription	HSMM	muscle
9	chr13:50019600-50036000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:50019800-50028400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:50019800-50028600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:50019800-50035200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:50019800-50035200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:50019800-50035200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:50019800-50035800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr13:50019800-50035800	Weak transcription	Fetal Muscle Leg	muscle
17	chr13:50019800-50037400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:50019800-50037400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr13:50020000-50035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:50020000-50035600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:50020000-50037200	Weak transcription	Right Ventricle	heart
22	chr13:50020200-50028200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr13:50020200-50028200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr13:50020200-50034600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:50020200-50035400	Weak transcription	Placenta	Placenta
26	chr13:50020200-50035800	Weak transcription	Pancreas	Pancrea
27	chr13:50020200-50068400	Weak transcription	HMEC	breast
28	chr13:50020600-50035800	Weak transcription	Thymus	Thymus
29	chr13:50021000-50035000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr13:50021000-50035800	Weak transcription	Fetal Intestine Small	intestine
31	chr13:50021200-50028800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr13:50021600-50035200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr13:50021800-50035800	Weak transcription	Brain Anterior Caudate	brain
34	chr13:50022000-50028200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:50022000-50028600	Weak transcription	Primary T cells from cord blood	blood
36	chr13:50022000-50032400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:50022000-50035200	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:50022000-50035600	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:50022000-50035800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
41	chr13:50022400-50031600	Weak transcription	Ovary	ovary
42	chr13:50022400-50035000	Weak transcription	Fetal Heart	heart
43	chr13:50022400-50035400	Weak transcription	K562	blood
44	chr13:50022800-50030600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr13:50023000-50030200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
47	chr13:50023200-50031000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr13:50024600-50028400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr13:50024600-50034800	Weak transcription	HepG2	liver
50	chr13:50024600-50035800	Weak transcription	HSMMtube	muscle

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