Variant report

Variant	rs1853829
Chromosome Location	chr13:50157827-50157828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50018389..50020157-chr13:50156893..50158971,2	MCF-7	breast:
2	chr13:50157525..50159034-chr13:50176178..50177840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11620566	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12429081	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12430435	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12431331	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1325659	0.90[AFR][1000 genomes]
rs13378867	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35472053	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851161	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4942853	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61961441	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7321549	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7332010	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7332029	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7332132	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7332641	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7333944	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995979	0.90[AFR][1000 genomes]
rs9316461	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316465	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9316466	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9591285	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9596157	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	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
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1853829	RCBTB1	cis	Whole Blood	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:50122000-50158000	Weak transcription	Brain Germinal Matrix	brain
3	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
4	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
8	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:50135600-50158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:50135600-50158400	Weak transcription	Osteobl	bone
11	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:50140800-50158000	Weak transcription	Fetal Brain Male	brain
13	chr13:50141200-50158000	Weak transcription	NHDF-Ad	bronchial
14	chr13:50141400-50158000	Weak transcription	Fetal Lung	lung
15	chr13:50141400-50158600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:50142000-50158000	Weak transcription	NHLF	lung
17	chr13:50142200-50158600	Weak transcription	K562	blood
18	chr13:50144600-50158400	Weak transcription	A549	lung
19	chr13:50144800-50158200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr13:50144800-50158200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:50145000-50158600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr13:50145800-50158000	Weak transcription	Hela-S3	cervix
23	chr13:50145800-50158200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:50149200-50158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr13:50151800-50158000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:50151800-50158000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:50151800-50158600	Weak transcription	Psoas Muscle	Psoas
28	chr13:50151800-50158600	Weak transcription	Right Ventricle	heart
29	chr13:50152000-50158600	Weak transcription	Aorta	Aorta
30	chr13:50154200-50158200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:50154200-50158600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:50154200-50159000	Weak transcription	Gastric	stomach
33	chr13:50154400-50158000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr13:50154400-50158000	Weak transcription	Adipose Nuclei	Adipose
35	chr13:50154400-50158200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:50154400-50158600	Weak transcription	HSMMtube	muscle
37	chr13:50154600-50158000	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:50154600-50158000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:50154600-50158600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr13:50154600-50158600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr13:50154600-50158600	Weak transcription	Liver	Liver
42	chr13:50154600-50158600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr13:50154600-50158600	Weak transcription	NH-A	brain
44	chr13:50154800-50158000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr13:50154800-50158000	Weak transcription	HUVEC	blood vessel
46	chr13:50154800-50158200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr13:50154800-50158400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr13:50154800-50158400	Weak transcription	HSMM	muscle
49	chr13:50154800-50158600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr13:50155000-50158000	Weak transcription	Primary hematopoietic stem cells	blood

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