Variant report

Variant	rs9562884
Chromosome Location	chr13:50041401-50041402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17381926	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41284778	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56737298	0.95[ASN][1000 genomes]
rs59837207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66771344	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67714799	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7317398	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73188659	0.82[EUR][1000 genomes]
rs73190705	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7331182	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9562880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9562888	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568205	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568207	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568209	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568210	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568227	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568231	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	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	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
12	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
13	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50020200-50068400	Weak transcription	HMEC	breast
2	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
3	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
4	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
5	chr13:50034400-50050800	Weak transcription	NHEK	skin
6	chr13:50034400-50052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:50034400-50068800	Weak transcription	NH-A	brain
8	chr13:50035200-50042000	Strong transcription	Colon Smooth Muscle	Colon
9	chr13:50035200-50042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
11	chr13:50036600-50068000	Weak transcription	K562	blood
12	chr13:50037000-50045600	Weak transcription	Fetal Heart	heart
13	chr13:50037800-50050200	Weak transcription	Osteobl	bone
14	chr13:50037800-50050600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:50037800-50050800	Weak transcription	Brain Angular Gyrus	brain
16	chr13:50037800-50051000	Weak transcription	Spleen	Spleen
17	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
19	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
20	chr13:50038000-50041600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr13:50038000-50041800	Strong transcription	Fetal Thymus	thymus
22	chr13:50038000-50043400	Weak transcription	Placenta	Placenta
23	chr13:50038000-50044600	Weak transcription	Fetal Stomach	stomach
24	chr13:50038000-50044600	Weak transcription	Lung	lung
25	chr13:50038000-50049000	Weak transcription	Gastric	stomach
26	chr13:50038000-50050200	Weak transcription	Esophagus	oesophagus
27	chr13:50038000-50050200	Weak transcription	HSMMtube	muscle
28	chr13:50038000-50050200	Weak transcription	NHLF	lung
29	chr13:50038000-50050800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr13:50038000-50051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr13:50038000-50062800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr13:50038000-50063400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr13:50038000-50063600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:50038000-50063800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr13:50038200-50046600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:50038200-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:50038200-50051000	Weak transcription	Aorta	Aorta
39	chr13:50038200-50054200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr13:50038200-50062400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:50038200-50063400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr13:50038400-50042000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr13:50038400-50042400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:50038400-50043400	Weak transcription	NHDF-Ad	bronchial
45	chr13:50038400-50044400	Weak transcription	Dnd41	blood
46	chr13:50038400-50044400	Weak transcription	GM12878-XiMat	blood
47	chr13:50038400-50045600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr13:50038400-50048400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr13:50038400-50048800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr13:50038400-50048800	Weak transcription	Right Ventricle	heart

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