Variant report

Variant	rs683319
Chromosome Location	chr18:9629590-9629591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9629058..9631077-chr18:9650339..9653253,2	K562	blood:
2	chr18:9613656..9616076-chr18:9629019..9630972,2	K562	blood:
3	chr18:9627920..9630651-chr18:9632769..9635738,3	K562	blood:
4	chr18:9613322..9616400-chr18:9628599..9633857,7	MCF-7	breast:
5	chr18:9616624..9619206-chr18:9627826..9630962,3	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11081489	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1662885	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787165	0.81[ASN][1000 genomes]
rs1787166	0.90[ASN][1000 genomes]
rs2028661	0.81[ASN][1000 genomes]
rs2028662	0.81[ASN][1000 genomes]
rs2028663	0.81[ASN][1000 genomes]
rs2289684	0.81[ASN][1000 genomes]
rs2903504	0.86[EUR][1000 genomes]
rs329002	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329004	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329023	0.92[EUR][1000 genomes]
rs329024	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329033	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35444634	0.81[ASN][1000 genomes]
rs428598	0.81[ASN][1000 genomes]
rs583306	0.81[ASN][1000 genomes]
rs586544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589559	0.90[ASN][1000 genomes]
rs599861	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs610564	0.89[EUR][1000 genomes]
rs62088919	0.86[AMR][1000 genomes]
rs62088920	0.81[ASN][1000 genomes]
rs638578	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs667695	0.81[ASN][1000 genomes]
rs671339	0.81[ASN][1000 genomes]
rs677461	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs680478	0.81[ASN][1000 genomes]
rs681297	0.81[ASN][1000 genomes]
rs694861	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233160	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7234128	0.90[ASN][1000 genomes]
rs8090919	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807604	0.81[ASN][1000 genomes]
rs9950583	0.90[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	nsv576449	chr18:9623052-9700382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs683319	RP11-692N5.1	cis	Nerve Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9617600-9630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:9627800-9630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:9627800-9630600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr18:9627800-9632200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr18:9628000-9630000	Weak transcription	NHDF-Ad	bronchial
6	chr18:9628000-9630400	Weak transcription	K562	blood
7	chr18:9628000-9630600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr18:9628000-9630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr18:9628000-9630600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:9628000-9630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:9628000-9631400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr18:9628000-9631400	Weak transcription	Osteobl	bone
13	chr18:9628000-9631600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr18:9628000-9631600	Weak transcription	A549	lung
15	chr18:9628000-9631800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:9628000-9631800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:9628000-9631800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:9628000-9631800	Weak transcription	NH-A	brain
19	chr18:9628000-9632200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr18:9628000-9642800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr18:9628200-9629800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr18:9628200-9630000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr18:9628200-9630000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr18:9628200-9630600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr18:9628200-9630600	Weak transcription	Hela-S3	cervix
26	chr18:9628200-9631000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:9628200-9631200	Weak transcription	NHLF	lung
28	chr18:9628200-9631600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:9628200-9631600	Weak transcription	HSMMtube	muscle
30	chr18:9628200-9631800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:9628200-9631800	Weak transcription	NHEK	skin
32	chr18:9628200-9632000	Weak transcription	HMEC	breast
33	chr18:9629200-9630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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