Variant report

Variant	rs1886793
Chromosome Location	chr13:50145449-50145450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50068857..50071479-chr13:50143285..50145487,2	MCF-7	breast:
2	chr13:50142756..50146527-chr13:50158016..50161593,4	MCF-7	breast:
3	chr13:50038641..50040451-chr13:50143314..50145864,2	MCF-7	breast:
4	chr13:50143262..50147042-chr13:50150087..50153613,4	MCF-7	breast:
5	chr13:50133873..50136164-chr13:50144707..50146572,2	MCF-7	breast:
6	chr13:50143614..50146624-chr13:50158019..50161696,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1198421	0.83[ASN][1000 genomes]
rs1198422	0.83[ASN][1000 genomes]
rs1359542	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1536192	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536195	0.86[EUR][1000 genomes]
rs1570883	0.86[EUR][1000 genomes]
rs1998780	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1998781	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2104183	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2146145	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2209506	0.86[EUR][1000 genomes]
rs2274278	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2274284	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2407697	0.84[EUR][1000 genomes]
rs2897741	0.82[EUR][1000 genomes]
rs3794376	0.86[EUR][1000 genomes]
rs4941648	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4941650	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5007254	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6561539	0.84[EUR][1000 genomes]
rs6561540	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6561542	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7139724	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7317140	0.82[EUR][1000 genomes]
rs7324024	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7983283	0.84[EUR][1000 genomes]
rs7986405	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7989286	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7992691	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7994516	0.86[EUR][1000 genomes]
rs7996012	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8000962	0.88[EUR][1000 genomes]
rs9526577	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535259	0.84[EUR][1000 genomes]
rs9535262	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9535269	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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
rs1886793	ARL11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50088400-50151000	Weak transcription	Psoas Muscle	Psoas
2	chr13:50108600-50158800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:50122000-50158000	Weak transcription	Brain Germinal Matrix	brain
4	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
5	chr13:50126400-50152400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:50129800-50155200	Weak transcription	Spleen	Spleen
8	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr13:50132400-50153600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr13:50132400-50153800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr13:50132400-50153800	Weak transcription	NH-A	brain
12	chr13:50133400-50154000	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:50134200-50151000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
16	chr13:50134400-50151000	Weak transcription	HSMMtube	muscle
17	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:50135200-50153400	Weak transcription	Gastric	stomach
19	chr13:50135200-50154000	Weak transcription	Placenta	Placenta
20	chr13:50135400-50145600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:50135600-50151000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:50135600-50151200	Weak transcription	Aorta	Aorta
23	chr13:50135600-50153800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr13:50135600-50155200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:50135600-50158000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:50135600-50158400	Weak transcription	Osteobl	bone
27	chr13:50135800-50153600	Weak transcription	HepG2	liver
28	chr13:50136200-50152200	Weak transcription	Primary B cells from cord blood	blood
29	chr13:50138200-50153400	Weak transcription	Thymus	Thymus
30	chr13:50138400-50153800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:50138600-50152200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:50138600-50157200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:50138800-50146200	Weak transcription	Fetal Stomach	stomach
34	chr13:50139200-50153000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:50139200-50153000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:50139200-50153200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:50139400-50153400	Weak transcription	Fetal Intestine Small	intestine
38	chr13:50139400-50153600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:50139600-50153400	Weak transcription	Lung	lung
41	chr13:50140800-50153800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:50140800-50154200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr13:50140800-50158000	Weak transcription	Fetal Brain Male	brain
44	chr13:50141000-50153200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:50141000-50153800	Weak transcription	Adipose Nuclei	Adipose
46	chr13:50141000-50153800	Weak transcription	Liver	Liver
47	chr13:50141200-50158000	Weak transcription	NHDF-Ad	bronchial
48	chr13:50141400-50151000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:50141400-50151000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr13:50141400-50152400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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