Variant report

Variant	rs56940858
Chromosome Location	chr13:97942695-97942696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:97875244..97877939-chr13:97941358..97944028,3	MCF-7	breast:
2	chr13:97924869..97926520-chr13:97941011..97942795,2	MCF-7	breast:
3	chr13:97942331..97944777-chr13:97956193..97959164,2	MCF-7	breast:
4	chr13:97942503..97945299-chr13:97946512..97948941,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10508030	0.82[EUR][1000 genomes]
rs10508031	0.82[EUR][1000 genomes]
rs12864731	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16951504	0.82[EUR][1000 genomes]
rs16954000	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16954002	0.82[EUR][1000 genomes]
rs17235614	0.83[ASN][1000 genomes]
rs17301362	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35039622	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35538229	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57526148	0.82[EUR][1000 genomes]
rs58421118	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59357402	0.82[EUR][1000 genomes]
rs61255793	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999038	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513227	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9513228	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9513229	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513230	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513231	0.91[ASN][1000 genomes]
rs9516891	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516895	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516896	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516897	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516898	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516899	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953504	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045777	chr13:97875574-97955134	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97914200-97960200	Weak transcription	Fetal Brain Male	brain
2	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr13:97929000-97947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:97929400-97955000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr13:97929600-97953400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:97929800-97953200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr13:97929800-97953400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:97931000-97953600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr13:97931200-97949000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:97933000-97947800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr13:97933000-97953600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr13:97933200-97943000	Weak transcription	Osteobl	bone
13	chr13:97933200-97946600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:97933200-97946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr13:97933200-97947400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr13:97933200-97949600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr13:97933200-97970400	Weak transcription	Placenta	Placenta
18	chr13:97933400-97952400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr13:97933600-97943200	Enhancers	Brain Hippocampus Middle	brain
20	chr13:97933600-97949200	Weak transcription	K562	blood
21	chr13:97933600-97953600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr13:97933800-97947000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:97934000-97954400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr13:97935600-97943000	Weak transcription	Esophagus	oesophagus
25	chr13:97935600-97947000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:97935600-97947200	Weak transcription	NHDF-Ad	bronchial
27	chr13:97935600-97954800	Weak transcription	Colonic Mucosa	Colon
28	chr13:97935800-97943000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:97935800-97943000	Weak transcription	NH-A	brain
30	chr13:97935800-97947400	Weak transcription	Stomach Mucosa	stomach
31	chr13:97935800-97949400	Weak transcription	Primary B cells from cord blood	blood
32	chr13:97936200-97943000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:97936200-97947200	Weak transcription	Aorta	Aorta
34	chr13:97936400-97943000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr13:97936400-97943000	Weak transcription	HMEC	breast
36	chr13:97936800-97946800	Weak transcription	Adipose Nuclei	Adipose
37	chr13:97936800-97947200	Weak transcription	Fetal Stomach	stomach
38	chr13:97936800-97949400	Weak transcription	Ovary	ovary
39	chr13:97936800-97949400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr13:97936800-97952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:97937000-97951400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr13:97937200-97947600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:97937600-97943000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr13:97938000-97947600	Weak transcription	Fetal Lung	lung
45	chr13:97938200-97945800	Weak transcription	HUVEC	blood vessel
46	chr13:97938200-97946600	Weak transcription	NHLF	lung
47	chr13:97938200-97947600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:97938400-97943000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:97938600-97947400	Weak transcription	Hela-S3	cervix
50	chr13:97938800-97947400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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