Variant report

Variant	rs9568269
Chromosome Location	chr13:50158142-50158143
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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11148155	0.85[EUR][1000 genomes]
rs11619565	0.81[EUR][1000 genomes]
rs12430463	0.81[EUR][1000 genomes]
rs4941647	0.82[CHB][hapmap]
rs56076648	0.81[EUR][1000 genomes]
rs59934906	0.81[EUR][1000 genomes]
rs61959865	0.81[EUR][1000 genomes]
rs61959868	0.81[EUR][1000 genomes]
rs61959873	0.81[EUR][1000 genomes]
rs61961440	0.81[EUR][1000 genomes]
rs73192614	0.81[EUR][1000 genomes]
rs73192638	0.81[EUR][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
rs9568269	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr13:50124000-50158800	Weak transcription	Esophagus	oesophagus
3	chr13:50129000-50158800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:50130400-50158800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr13:50134200-50158400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr13:50134200-50158400	Weak transcription	Fetal Brain Female	brain
7	chr13:50135000-50158600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr13:50135600-50158400	Weak transcription	Osteobl	bone
9	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr13:50141400-50158600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr13:50142200-50158600	Weak transcription	K562	blood
12	chr13:50144600-50158400	Weak transcription	A549	lung
13	chr13:50144800-50158200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:50144800-50158200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr13:50145000-50158600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr13:50145800-50158200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:50149200-50158600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr13:50151800-50158600	Weak transcription	Psoas Muscle	Psoas
19	chr13:50151800-50158600	Weak transcription	Right Ventricle	heart
20	chr13:50152000-50158600	Weak transcription	Aorta	Aorta
21	chr13:50154200-50158200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:50154200-50158600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr13:50154200-50159000	Weak transcription	Gastric	stomach
24	chr13:50154400-50158200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr13:50154400-50158600	Weak transcription	HSMMtube	muscle
26	chr13:50154600-50158600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr13:50154600-50158600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:50154600-50158600	Weak transcription	Liver	Liver
29	chr13:50154600-50158600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr13:50154600-50158600	Weak transcription	NH-A	brain
31	chr13:50154800-50158200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr13:50154800-50158400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr13:50154800-50158400	Weak transcription	HSMM	muscle
34	chr13:50154800-50158600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr13:50155200-50158600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:50155200-50158800	Weak transcription	Placenta	Placenta
37	chr13:50155200-50159000	Weak transcription	Pancreas	Pancrea
38	chr13:50155400-50158400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:50155600-50158600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr13:50155600-50158600	Weak transcription	Fetal Intestine Large	intestine
41	chr13:50155600-50158800	Weak transcription	Left Ventricle	heart
42	chr13:50155800-50158400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:50155800-50158400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr13:50155800-50158400	Weak transcription	GM12878-XiMat	blood
45	chr13:50155800-50158600	Weak transcription	Primary B cells from cord blood	blood
46	chr13:50156000-50158200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr13:50156000-50158200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:50156000-50158200	Weak transcription	Fetal Thymus	thymus
49	chr13:50156000-50158400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:50156000-50158600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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