Variant report

Variant	rs680478
Chromosome Location	chr18:9609957-9609958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9607097..9610234-chr18:9611887..9616228,7	MCF-7	breast:
2	chr18:9598014..9601741-chr18:9607589..9612497,6	MCF-7	breast:
3	chr18:9608061..9610764-chr18:9617117..9619483,2	MCF-7	breast:
4	chr18:9595087..9597869-chr18:9607007..9610720,3	MCF-7	breast:
5	chr18:9606592..9610420-chr18:9613242..9616597,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263627	Chromatin interaction
ENSG00000212572	Chromatin interaction
ENSG00000154845	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11081489	0.81[ASN][1000 genomes]
rs1662885	0.89[ASN][1000 genomes]
rs1787165	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787166	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028661	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028662	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028663	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289684	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329002	1.00[ASN][1000 genomes]
rs329004	1.00[ASN][1000 genomes]
rs329008	0.89[ASN][1000 genomes]
rs329023	0.90[ASN][1000 genomes]
rs329024	1.00[ASN][1000 genomes]
rs329033	1.00[ASN][1000 genomes]
rs35444634	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407530	0.89[ASN][1000 genomes]
rs428598	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583306	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586544	0.81[ASN][1000 genomes]
rs589559	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599861	1.00[ASN][1000 genomes]
rs610564	0.82[ASN][1000 genomes]
rs62088920	0.81[ASN][1000 genomes]
rs638578	0.89[ASN][1000 genomes]
rs667695	1.00[ASN][1000 genomes]
rs671339	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677461	0.85[ASN][1000 genomes]
rs681297	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683319	0.81[ASN][1000 genomes]
rs694861	0.89[ASN][1000 genomes]
rs7233160	1.00[ASN][1000 genomes]
rs7234128	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7359735	0.88[EUR][1000 genomes]
rs8088389	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090919	0.89[ASN][1000 genomes]
rs9807577	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807604	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807610	0.83[EUR][1000 genomes]
rs9807614	0.82[EUR][1000 genomes]
rs9950583	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs680478	RP11-692N5.1	cis	Esophagus Mucosa	GTEx
rs680478	RP11-692N5.1	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:9589000-9611000	Weak transcription	Lung	lung
5	chr18:9594200-9613600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:9595200-9612000	Weak transcription	Esophagus	oesophagus
7	chr18:9596000-9611000	Weak transcription	Gastric	stomach
8	chr18:9597200-9611000	Weak transcription	NH-A	brain
9	chr18:9597400-9613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:9598000-9612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr18:9601400-9610800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr18:9601600-9610800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr18:9601800-9610400	Weak transcription	Fetal Stomach	stomach
14	chr18:9601800-9612200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr18:9603200-9610800	Weak transcription	Placenta	Placenta
16	chr18:9603200-9611000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr18:9603600-9611000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr18:9603800-9611000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:9604200-9611000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr18:9604400-9610800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:9604400-9611000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr18:9604600-9610800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr18:9604600-9611000	Weak transcription	Primary B cells from cord blood	blood
24	chr18:9604600-9611000	Weak transcription	Spleen	Spleen
25	chr18:9604800-9612200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr18:9604800-9612400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr18:9605000-9611200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr18:9605200-9610800	Weak transcription	Fetal Intestine Large	intestine
29	chr18:9605600-9611600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr18:9606000-9611000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr18:9606600-9611000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:9606600-9611000	Weak transcription	HSMMtube	muscle
33	chr18:9607200-9613400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr18:9607600-9610400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr18:9607800-9610800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:9608000-9611200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr18:9608000-9611600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr18:9608200-9610000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr18:9608200-9610000	Enhancers	Liver	Liver
40	chr18:9608200-9610400	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr18:9608200-9610400	Enhancers	HUVEC	blood vessel
42	chr18:9608200-9613600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr18:9608400-9610000	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr18:9608600-9610200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr18:9608600-9611000	Weak transcription	Brain Anterior Caudate	brain
46	chr18:9608600-9611400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr18:9608800-9610000	Enhancers	Muscle Satellite Cultured Cells	--
48	chr18:9608800-9610200	Enhancers	Hela-S3	cervix
49	chr18:9608800-9611000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr18:9609000-9612200	Weak transcription	Fetal Kidney	kidney

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