Variant report

Variant	rs11840676
Chromosome Location	chr13:48809556-48809557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48806544..48809798-chr13:48876519..48878974,4	K562	blood:
3	chr13:48801755..48804565-chr13:48807877..48810629,2	K562	blood:
4	chr13:48808662..48812732-chr13:48820679..48824988,4	K562	blood:
5	chr13:48807403..48809674-chr13:48828409..48830579,2	K562	blood:
6	chr13:48803757..48809033-chr13:48809443..48816513,10	MCF-7	breast:
7	chr13:48806625..48809806-chr13:48877426..48879405,3	K562	blood:
8	chr13:48575152..48576683-chr13:48807803..48809574,2	K562	blood:
9	chr13:48807837..48812135-chr13:48876736..48879539,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227848	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000139687	Chromatin interaction
ENSG00000231473	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs171989	0.92[EUR][1000 genomes]
rs185587	0.84[EUR][1000 genomes]
rs198559	0.92[EUR][1000 genomes]
rs198565	0.92[EUR][1000 genomes]
rs198566	0.92[EUR][1000 genomes]
rs198567	0.92[EUR][1000 genomes]
rs198572	0.92[EUR][1000 genomes]
rs198573	0.92[EUR][1000 genomes]
rs198600	0.92[EUR][1000 genomes]
rs198601	0.92[EUR][1000 genomes]
rs198613	0.92[EUR][1000 genomes]
rs198616	0.92[EUR][1000 genomes]
rs198617	0.92[EUR][1000 genomes]
rs198618	0.92[EUR][1000 genomes]
rs198628	0.92[EUR][1000 genomes]
rs198632	0.92[EUR][1000 genomes]
rs198636	0.92[EUR][1000 genomes]
rs2245534	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2265777	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2406932	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2515668	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804082	0.92[EUR][1000 genomes]
rs2804084	0.92[EUR][1000 genomes]
rs2804085	0.92[EUR][1000 genomes]
rs2804086	0.92[EUR][1000 genomes]
rs2804087	0.92[EUR][1000 genomes]
rs2804088	0.92[EUR][1000 genomes]
rs2804089	0.92[EUR][1000 genomes]
rs2804091	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804092	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854352	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854356	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854363	0.92[EUR][1000 genomes]
rs2854364	0.92[EUR][1000 genomes]
rs2854365	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs411661	0.84[EUR][1000 genomes]
rs411862	0.92[EUR][1000 genomes]
rs4151590	0.84[EUR][1000 genomes]
rs416156	0.92[EUR][1000 genomes]
rs428431	0.92[EUR][1000 genomes]
rs4625624	1.00[EUR][1000 genomes]
rs547747	0.92[EUR][1000 genomes]
rs61507973	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7318012	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7990103	0.92[EUR][1000 genomes]
rs8001351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9285166	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316371	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9332248	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9332281	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9562817	0.92[EUR][1000 genomes]
rs9591153	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591154	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591155	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591163	0.92[EUR][1000 genomes]
rs9595872	0.83[EUR][1000 genomes]
rs9595894	0.92[EUR][1000 genomes]
rs9595909	0.92[EUR][1000 genomes]
rs9595910	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48806200-48809800	Active TSS	Brain Angular Gyrus	brain
2	chr13:48806600-48809800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr13:48806600-48809800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr13:48806600-48809800	Active TSS	Brain Substantia Nigra	brain
5	chr13:48806600-48810000	Active TSS	Colonic Mucosa	Colon
6	chr13:48806600-48810000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr13:48806600-48810000	Active TSS	NHLF	lung
8	chr13:48806600-48810400	Active TSS	Aorta	Aorta
9	chr13:48806600-48811000	Active TSS	Psoas Muscle	Psoas
10	chr13:48806600-48811000	Active TSS	Right Ventricle	heart
11	chr13:48806600-48812200	Active TSS	Ovary	ovary
12	chr13:48806600-48812200	Active TSS	Right Atrium	heart
13	chr13:48806800-48809800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr13:48806800-48809800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr13:48806800-48809800	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr13:48806800-48810000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr13:48806800-48810000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:48806800-48810000	Active TSS	Colon Smooth Muscle	Colon
19	chr13:48806800-48810200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr13:48806800-48810200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr13:48806800-48810400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr13:48806800-48810400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:48806800-48810600	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr13:48807000-48809600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:48807000-48809600	Active TSS	Adipose Nuclei	Adipose
26	chr13:48807000-48809600	Active TSS	Fetal Muscle Trunk	muscle
27	chr13:48807000-48809800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:48807000-48809800	Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr13:48807000-48809800	Active TSS	Brain Cingulate Gyrus	brain
30	chr13:48807000-48809800	Active TSS	Fetal Intestine Small	intestine
31	chr13:48807000-48809800	Active TSS	Fetal Muscle Leg	muscle
32	chr13:48807000-48809800	Active TSS	Rectal Smooth Muscle	rectum
33	chr13:48807000-48809800	Active TSS	HMEC	breast
34	chr13:48807000-48809800	Active TSS	NHEK	skin
35	chr13:48807000-48810000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:48807000-48810000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:48807000-48810000	Active TSS	Brain Anterior Caudate	brain
38	chr13:48807000-48810000	Active TSS	Duodenum Mucosa	Duodenum
39	chr13:48807000-48810000	Active TSS	NHDF-Ad	bronchial
40	chr13:48807000-48810200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr13:48807000-48810200	Active TSS	Stomach Smooth Muscle	stomach
42	chr13:48807000-48810400	Active TSS	Fetal Stomach	stomach
43	chr13:48807000-48811200	Active TSS	Thymus	Thymus
44	chr13:48807200-48809600	Active TSS	HSMMtube	muscle
45	chr13:48807800-48809600	Active TSS	Fetal Brain Female	brain
46	chr13:48807800-48809800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:48807800-48810000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:48808000-48809600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:48808200-48809800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr13:48808200-48810200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood

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