Variant report

Variant	rs6561540
Chromosome Location	chr13:50118118-50118119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50022863..50025187-chr13:50116857..50119478,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1359542	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1536192	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1536195	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570883	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886793	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1977353	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1998780	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998781	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104183	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2146145	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2274278	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274284	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407697	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897741	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794376	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941648	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4941650	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs5007254	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6561539	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561542	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139724	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7317140	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324024	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7325207	0.88[EUR][1000 genomes]
rs7983283	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7986405	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7989286	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7992396	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7992691	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7996012	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8000962	0.80[EUR][1000 genomes]
rs9526577	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535259	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535262	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535269	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1052801	chr13:50116407-50144995	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6561540	RCBTB1	Cis_1M	lymphoblastoid	RTeQTL
rs6561540	ARL11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
2	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
3	chr13:50088600-50134200	Weak transcription	Stomach Mucosa	stomach
4	chr13:50090000-50122800	Weak transcription	Ovary	ovary
5	chr13:50090000-50123600	Weak transcription	Esophagus	oesophagus
6	chr13:50091400-50138800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:50094600-50120000	Weak transcription	Spleen	Spleen
8	chr13:50094600-50141600	Weak transcription	Right Ventricle	heart
9	chr13:50095000-50120400	Weak transcription	A549	lung
10	chr13:50097800-50135000	Weak transcription	Colonic Mucosa	Colon
11	chr13:50101600-50142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:50104600-50143800	Weak transcription	Hela-S3	cervix
13	chr13:50106600-50133200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:50109200-50121600	Weak transcription	Brain Germinal Matrix	brain
16	chr13:50110400-50134400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:50110600-50124800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:50110800-50126800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr13:50111400-50127600	Weak transcription	Fetal Heart	heart
20	chr13:50111600-50136600	Strong transcription	Dnd41	blood
21	chr13:50111800-50133200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:50112000-50118200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr13:50112000-50118400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:50112000-50135000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:50112200-50118200	Strong transcription	Fetal Muscle Leg	muscle
26	chr13:50112200-50121200	Strong transcription	Fetal Intestine Large	intestine
27	chr13:50112200-50134200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr13:50112200-50138400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:50112400-50118200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:50113200-50118200	Strong transcription	NHEK	skin
31	chr13:50113200-50121400	Strong transcription	HMEC	breast
32	chr13:50113200-50127200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:50113600-50123400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr13:50114000-50125800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr13:50114000-50126600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:50114200-50120000	Weak transcription	Brain Anterior Caudate	brain
37	chr13:50115000-50118800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:50115000-50119400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr13:50115000-50119400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:50115000-50119400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr13:50115000-50119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr13:50115000-50120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:50115000-50120000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr13:50115000-50120200	Weak transcription	Lung	lung
45	chr13:50115000-50123400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:50115000-50123400	Weak transcription	NHLF	lung
47	chr13:50115000-50123600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:50115000-50123800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr13:50115000-50132200	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:50115000-50140400	Weak transcription	Fetal Brain Male	brain

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