Variant report

Variant	rs11662617
Chromosome Location	chr18:13253598-13253599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13217260..13220397-chr18:13252163..13256866,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10445419	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10445429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10445430	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11080639	0.86[ASW][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.85[YRI][hapmap]
rs11659870	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11661574	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11665438	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12607576	0.86[ASW][hapmap]
rs55809306	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6505792	0.81[ASN][1000 genomes]
rs9652933	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:13233000-13260200	Weak transcription	Colonic Mucosa	Colon
5	chr18:13233400-13254000	Weak transcription	Spleen	Spleen
6	chr18:13233400-13259000	Weak transcription	Primary T cells from cord blood	blood
7	chr18:13236200-13258800	Weak transcription	Fetal Lung	lung
8	chr18:13237400-13258800	Weak transcription	Adipose Nuclei	Adipose
9	chr18:13237400-13258800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:13237800-13258800	Weak transcription	Colon Smooth Muscle	Colon
11	chr18:13239600-13255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr18:13240200-13256000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr18:13243200-13260200	Weak transcription	Aorta	Aorta
14	chr18:13243600-13278200	Weak transcription	Dnd41	blood
15	chr18:13246600-13256200	Weak transcription	Psoas Muscle	Psoas
16	chr18:13248400-13259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:13252400-13254600	Enhancers	Left Ventricle	heart
18	chr18:13252400-13257000	Enhancers	Fetal Heart	heart
19	chr18:13252600-13257000	Strong transcription	Thymus	Thymus
20	chr18:13252800-13253600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:13252800-13253600	Genic enhancers	Fetal Thymus	thymus
22	chr18:13252800-13254600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr18:13252800-13256200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:13253000-13253800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:13253000-13256400	Weak transcription	Fetal Muscle Leg	muscle
26	chr18:13253000-13267800	Weak transcription	Gastric	stomach
27	chr18:13253200-13253600	Enhancers	Brain Cingulate Gyrus	brain
28	chr18:13253200-13253600	Enhancers	Brain Hippocampus Middle	brain
29	chr18:13253200-13254200	Enhancers	Right Atrium	heart
30	chr18:13253200-13257400	Weak transcription	Esophagus	oesophagus
31	chr18:13253200-13259000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:13253200-13259800	Weak transcription	Brain Substantia Nigra	brain
33	chr18:13253200-13260000	Weak transcription	Brain Angular Gyrus	brain
34	chr18:13253400-13253600	Enhancers	Brain Germinal Matrix	brain
35	chr18:13253400-13253600	Enhancers	Fetal Brain Female	brain
36	chr18:13253400-13253800	Weak transcription	Right Ventricle	heart
37	chr18:13253400-13255400	Weak transcription	Fetal Brain Male	brain
38	chr18:13253400-13256200	Weak transcription	Brain Anterior Caudate	brain
39	chr18:13253400-13257400	Weak transcription	Lung	lung
40	chr18:13253400-13258800	Weak transcription	Brain Inferior Temporal Lobe	brain

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