Variant report

Variant	rs671339
Chromosome Location	chr18:9618005-9618006
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	chr18:9616424..9618415-chr18:9912586..9915951,3	MCF-7	breast:
2	chr18:9614482..9616420-chr18:9617986..9621274,5	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000272799	Chromatin interaction
ENSG00000101558	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787166	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028661	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028663	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289684	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407530	0.89[ASN][1000 genomes]
rs428598	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583306	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586544	0.81[ASN][1000 genomes]
rs589559	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs599861	1.00[ASN][1000 genomes]
rs610564	0.82[ASN][1000 genomes]
rs62088920	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs638578	0.89[ASN][1000 genomes]
rs667695	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677461	0.85[ASN][1000 genomes]
rs680478	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7359735	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8088389	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090919	0.89[ASN][1000 genomes]
rs9807577	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9807604	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807610	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9807614	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9950583	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1820504	chr18:9614250-9621841	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1801741	chr18:9614451-9621841	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv521175	chr18:9615851-9623052	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs671339	RP11-692N5.1	cis	lung	GTEx
rs671339	RP11-692N5.1	cis	Adipose Subcutaneous	GTEx
rs671339	RP11-692N5.1	cis	Skin Sun Exposed Lower leg	GTEx
rs671339	RP11-692N5.1	cis	Nerve Tibial	GTEx
rs671339	RP11-692N5.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9615400-9618200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:9615600-9619200	Weak transcription	GM12878-XiMat	blood
3	chr18:9615800-9619200	Weak transcription	Brain Angular Gyrus	brain
4	chr18:9615800-9619200	Weak transcription	Brain Anterior Caudate	brain
5	chr18:9615800-9619200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr18:9615800-9619200	Weak transcription	Esophagus	oesophagus
7	chr18:9615800-9619200	Enhancers	HUVEC	blood vessel
8	chr18:9615800-9619400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr18:9615800-9619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr18:9615800-9619600	Weak transcription	Fetal Lung	lung
11	chr18:9615800-9619800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:9615800-9625200	Weak transcription	Placenta	Placenta
13	chr18:9615800-9625400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr18:9615800-9627400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr18:9616000-9618800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr18:9616000-9619200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr18:9616000-9619200	Weak transcription	Stomach Mucosa	stomach
18	chr18:9616000-9619200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr18:9616000-9619800	Weak transcription	Brain Hippocampus Middle	brain
20	chr18:9616200-9619000	Weak transcription	HSMMtube	muscle
21	chr18:9616200-9619200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr18:9616200-9619200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr18:9616200-9619200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:9616200-9619400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:9616200-9619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr18:9616200-9619600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr18:9616800-9619400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr18:9617000-9619200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr18:9617000-9619200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:9617200-9618800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr18:9617200-9619200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr18:9617200-9619400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr18:9617400-9619000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:9617400-9619000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:9617400-9619000	Weak transcription	NH-A	brain
36	chr18:9617400-9619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:9617400-9619200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr18:9617400-9619200	Weak transcription	A549	lung
39	chr18:9617400-9619200	Weak transcription	Hela-S3	cervix
40	chr18:9617400-9619200	Weak transcription	NHDF-Ad	bronchial
41	chr18:9617400-9619200	Weak transcription	NHLF	lung
42	chr18:9617400-9619200	Weak transcription	Osteobl	bone
43	chr18:9617400-9619400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr18:9617400-9619400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr18:9617400-9619600	Weak transcription	HSMM	muscle
46	chr18:9617400-9619800	Weak transcription	K562	blood
47	chr18:9617400-9625400	Weak transcription	HMEC	breast
48	chr18:9617600-9619000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:9617600-9619200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr18:9617600-9619200	Weak transcription	Muscle Satellite Cultured Cells	--

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