Variant report

Variant	rs57783887
Chromosome Location	chr13:50263289-50263290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50261388..50263430-chr13:50264795..50266652,2	K562	blood:
2	chr13:50219670..50221939-chr13:50262892..50264928,2	K562	blood:
3	chr13:50258208..50260676-chr13:50262902..50265227,2	K562	blood:
4	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
5	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:
6	chr13:50262508..50268089-chr13:50363531..50368771,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction
ENSG00000123179	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1043729	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12584003	0.83[EUR][1000 genomes]
rs13313256	0.92[EUR][1000 genomes]
rs17073322	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17073347	0.92[EUR][1000 genomes]
rs17073356	0.92[EUR][1000 genomes]
rs1819191	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1885723	0.84[EUR][1000 genomes]
rs1969739	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998363	0.92[EUR][1000 genomes]
rs2181184	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236326	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736830	0.95[ASN][1000 genomes]
rs3742094	0.84[EUR][1000 genomes]
rs3782929	0.92[EUR][1000 genomes]
rs4941655	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4941656	0.84[EUR][1000 genomes]
rs4942862	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4942865	0.84[EUR][1000 genomes]
rs56738401	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57118905	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57794226	0.92[EUR][1000 genomes]
rs58124341	0.84[EUR][1000 genomes]
rs60019803	0.92[EUR][1000 genomes]
rs60106669	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60856213	0.92[EUR][1000 genomes]
rs7321391	0.84[EUR][1000 genomes]
rs7334018	0.92[EUR][1000 genomes]
rs7335016	0.84[EUR][1000 genomes]
rs7335310	0.92[EUR][1000 genomes]
rs73483835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73485710	0.84[EUR][1000 genomes]
rs765291	0.80[EUR][1000 genomes]
rs765292	0.84[EUR][1000 genomes]
rs7984711	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7988114	0.83[EUR][1000 genomes]
rs7989633	0.84[EUR][1000 genomes]
rs7990293	0.85[ASN][1000 genomes]
rs7993631	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7993860	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7994062	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535306	0.96[ASN][1000 genomes]
rs9591293	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591294	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9591296	0.92[EUR][1000 genomes]
rs9596172	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596173	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596174	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596175	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596176	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596181	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9596188	0.92[EUR][1000 genomes]
rs9596189	0.92[EUR][1000 genomes]
rs9596194	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
2	chr13:50242200-50264200	Weak transcription	K562	blood
3	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
7	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
9	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
12	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
15	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
16	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
18	chr13:50251800-50263600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:50253800-50264000	Weak transcription	Ovary	ovary
21	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:50254400-50264400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr13:50254400-50264400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr13:50254400-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:50254400-50264600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:50254400-50264600	Weak transcription	Esophagus	oesophagus
29	chr13:50254600-50264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:50255200-50264400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr13:50256200-50264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:50256400-50263800	Weak transcription	NH-A	brain
33	chr13:50256400-50263800	Weak transcription	NHLF	lung
34	chr13:50256400-50264400	Weak transcription	Brain Hippocampus Middle	brain
35	chr13:50256400-50264400	Weak transcription	Colonic Mucosa	Colon
36	chr13:50256400-50264400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr13:50256400-50264400	Weak transcription	NHDF-Ad	bronchial
38	chr13:50256600-50264200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:50256600-50264400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr13:50256600-50264400	Weak transcription	Brain Germinal Matrix	brain
41	chr13:50256600-50264600	Weak transcription	Placenta	Placenta
42	chr13:50256800-50263400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr13:50257000-50264000	Weak transcription	Fetal Brain Male	brain
44	chr13:50257200-50264400	Weak transcription	Fetal Brain Female	brain
45	chr13:50258200-50264400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr13:50258800-50263600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr13:50259000-50263600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:50259200-50263400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:50259200-50263600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:50259200-50264000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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