Variant report

Variant	rs6505769
Chromosome Location	chr18:12882749-12882750
allele	A/G
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:65596946..65598700-chr18:12882626..12885488,2	MCF-7	breast:
2	chr18:12843323..12846138-chr18:12882410..12884352,2	MCF-7	breast:
3	chr18:12862494..12865307-chr18:12880258..12883236,3	MCF-7	breast:
4	chr18:12880282..12885478-chr18:12946145..12950206,8	K562	blood:
5	chr18:12699803..12702594-chr18:12881299..12884040,2	K562	blood:
6	chr18:12882667..12884316-chr18:13724618..13726583,2	K562	blood:
7	chr18:12880787..12883002-chr4:37479463..37481440,2	MCF-7	breast:
8	chr18:12702487..12704134-chr18:12881395..12884232,2	MCF-7	breast:
9	chr18:12869114..12870887-chr18:12882231..12883982,2	K562	blood:
10	chr18:12699667..12702594-chr18:12881299..12884281,3	K562	blood:
11	chr18:12880282..12884361-chr18:12946145..12949673,9	K562	blood:
12	chr18:12880723..12883598-chr18:12902234..12904693,2	K562	blood:
13	chr18:12882295..12883903-chr18:12953395..12955724,2	K562	blood:
14	chr18:12808897..12811465-chr18:12881476..12883993,2	MCF-7	breast:
15	chr18:12657085..12659648-chr18:12882376..12884207,2	K562	blood:
16	chr18:12827164..12830026-chr18:12882449..12884069,2	K562	blood:
17	chr18:12865974..12868849-chr18:12882069..12883733,2	MCF-7	breast:
18	chr18:12881395..12884200-chr18:12946697..12949759,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000175354	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000177150	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2292758	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3826556	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45579734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471401	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797707	0.82[ASN][1000 genomes]
rs4797708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507304	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56384328	0.88[ASN][1000 genomes]
rs578377	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58200120	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59471125	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs607906	0.85[ASN][1000 genomes]
rs60803113	0.88[ASN][1000 genomes]
rs622717	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs637643	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs669822	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs670671	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683468	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7238238	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7241650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872144	0.87[ASN][1000 genomes]
rs73950681	0.83[ASN][1000 genomes]
rs73950683	0.85[ASN][1000 genomes]
rs73950684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73950685	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8084365	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8091305	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8098730	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9954778	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9959061	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961827	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961931	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9966378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12865800-12883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12875600-12882800	Enhancers	Primary B cells from peripheral blood	blood
3	chr18:12878600-12882800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr18:12878600-12882800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
5	chr18:12878800-12882800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr18:12879000-12882800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr18:12879200-12882800	Enhancers	Liver	Liver
8	chr18:12879600-12882800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr18:12879600-12883200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr18:12879800-12882800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:12879800-12882800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr18:12880400-12883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:12880600-12882800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr18:12880600-12883000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr18:12880600-12883000	Weak transcription	Left Ventricle	heart
16	chr18:12880800-12882800	Enhancers	Primary B cells from cord blood	blood
17	chr18:12880800-12882800	Weak transcription	Colonic Mucosa	Colon
18	chr18:12881200-12882800	Enhancers	Adipose Nuclei	Adipose
19	chr18:12881200-12883200	Weak transcription	Spleen	Spleen
20	chr18:12881600-12882800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr18:12881600-12882800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr18:12881600-12882800	Enhancers	Fetal Intestine Small	intestine
23	chr18:12881600-12882800	Enhancers	HSMMtube	muscle
24	chr18:12881600-12883000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr18:12881600-12883000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr18:12881600-12883000	Enhancers	Small Intestine	intestine
27	chr18:12881600-12883200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr18:12881800-12882800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr18:12881800-12882800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr18:12881800-12882800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr18:12881800-12883000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:12881800-12883000	Weak transcription	Lung	lung
33	chr18:12881800-12883000	Flanking Active TSS	K562	blood
34	chr18:12882000-12882800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr18:12882000-12882800	Enhancers	Colon Smooth Muscle	Colon
36	chr18:12882000-12883000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr18:12882000-12883200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr18:12882000-12883200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:12882000-12883400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr18:12882200-12882800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:12882200-12882800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr18:12882200-12882800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:12882200-12882800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:12882200-12882800	Enhancers	Fetal Heart	heart
45	chr18:12882200-12882800	Enhancers	Rectal Smooth Muscle	rectum
46	chr18:12882200-12882800	Weak transcription	Right Atrium	heart
47	chr18:12882200-12883000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr18:12882200-12883000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12882200-12883000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr18:12882200-12883000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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