Variant report

Variant	rs61957254
Chromosome Location	chr13:52756916-52756917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1122934	1.00[ASN][1000 genomes]
rs4091568	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941729	1.00[ASN][1000 genomes]
rs55667430	0.87[ASN][1000 genomes]
rs55715265	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345934	1.00[ASN][1000 genomes]
rs61957231	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957232	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957233	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61957238	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957248	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957249	1.00[ASN][1000 genomes]
rs61957252	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957253	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957255	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957256	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61957258	1.00[ASN][1000 genomes]
rs61957297	1.00[ASN][1000 genomes]
rs61957307	0.87[EUR][1000 genomes]
rs61958782	1.00[ASN][1000 genomes]
rs61958784	1.00[ASN][1000 genomes]
rs61958786	1.00[ASN][1000 genomes]
rs61958788	1.00[ASN][1000 genomes]
rs61958800	1.00[ASN][1000 genomes]
rs61958801	1.00[ASN][1000 genomes]
rs61958802	1.00[ASN][1000 genomes]
rs61958803	1.00[ASN][1000 genomes]
rs61958806	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958860	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958863	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958865	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719349	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333070	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73502305	1.00[ASN][1000 genomes]
rs73502307	1.00[ASN][1000 genomes]
rs9526818	1.00[ASN][1000 genomes]
rs9526840	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535814	1.00[ASN][1000 genomes]
rs9535818	1.00[ASN][1000 genomes]
rs9535831	1.00[ASN][1000 genomes]
rs9535838	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535839	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535850	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535852	1.00[ASN][1000 genomes]
rs9535859	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535869	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535870	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535875	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535881	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535886	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535890	1.00[ASN][1000 genomes]
rs9535892	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535893	1.00[ASN][1000 genomes]
rs9535894	1.00[ASN][1000 genomes]
rs9535897	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535900	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535901	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535902	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535903	1.00[ASN][1000 genomes]
rs9535906	1.00[ASN][1000 genomes]
rs9535909	1.00[ASN][1000 genomes]
rs9535910	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535911	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535913	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9536044	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv976116	chr13:52741751-52768674	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52733800-52757000	Weak transcription	Spleen	Spleen
2	chr13:52734000-52760000	Weak transcription	Gastric	stomach
3	chr13:52734400-52761000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:52734400-52768000	Weak transcription	Aorta	Aorta
5	chr13:52734600-52766000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:52736400-52767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:52736800-52765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:52737200-52767400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:52738400-52767400	Weak transcription	HMEC	breast
10	chr13:52739200-52761400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:52739600-52760400	Strong transcription	Fetal Thymus	thymus
12	chr13:52739800-52758000	Weak transcription	Stomach Mucosa	stomach
13	chr13:52740000-52762800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr13:52740000-52764600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:52740000-52767200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:52741000-52767800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:52741200-52763600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr13:52741400-52759600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr13:52741800-52760200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr13:52743400-52767600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:52743400-52767800	Weak transcription	Esophagus	oesophagus
22	chr13:52743400-52768200	Weak transcription	Small Intestine	intestine
23	chr13:52745600-52767400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr13:52747400-52767200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:52748400-52758200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr13:52749200-52765600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr13:52749800-52757600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr13:52751400-52760400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:52752400-52760200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:52752600-52767200	Weak transcription	Psoas Muscle	Psoas
31	chr13:52753600-52758800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:52753800-52759200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:52754400-52758200	Weak transcription	Fetal Brain Female	brain
34	chr13:52754400-52758600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52754400-52767200	Weak transcription	Colonic Mucosa	Colon
36	chr13:52754400-52767800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr13:52754600-52757000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:52754600-52757000	Weak transcription	Fetal Intestine Large	intestine
39	chr13:52754600-52757000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr13:52754600-52757200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:52754600-52757400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr13:52754600-52757800	Weak transcription	Primary B cells from cord blood	blood
43	chr13:52754600-52758000	Weak transcription	Dnd41	blood
44	chr13:52754600-52758000	Weak transcription	K562	blood
45	chr13:52754600-52758200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:52754600-52758200	Weak transcription	Brain Anterior Caudate	brain
47	chr13:52754600-52758200	Weak transcription	Brain Hippocampus Middle	brain
48	chr13:52754600-52758200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:52754600-52758200	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:52754600-52758200	Weak transcription	Stomach Smooth Muscle	stomach

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