Variant report

Variant	rs12969241
Chromosome Location	chr18:12842480-12842481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12836859..12842714-chr18:12880630..12885724,12	MCF-7	breast:
2	chr18:12828322..12831138-chr18:12840909..12843009,2	K562	blood:
3	chr18:12838530..12843294-chr18:12882526..12884530,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12955302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963474	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12964314	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12968719	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34153303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34416003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34799913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35320197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35923716	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35954636	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35967540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71353227	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:12828400-12842600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
6	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
7	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
8	chr18:12834200-12850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr18:12838600-12843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:12838600-12843000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr18:12838600-12843000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:12838600-12843400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr18:12838600-12843400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:12838600-12843400	Weak transcription	Gastric	stomach
15	chr18:12838600-12848400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:12838600-12851800	Weak transcription	Fetal Brain Male	brain
17	chr18:12838600-12852000	Weak transcription	Ovary	ovary
18	chr18:12838600-12854000	Weak transcription	Left Ventricle	heart
19	chr18:12838600-12856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:12838600-12856200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr18:12838600-12857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:12838600-12862400	Weak transcription	NH-A	brain
25	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr18:12838800-12842600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr18:12838800-12842800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr18:12838800-12851800	Weak transcription	Fetal Lung	lung
29	chr18:12838800-12852600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr18:12838800-12854600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr18:12838800-12855600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
33	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:12839600-12842600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr18:12839600-12851600	Weak transcription	HSMMtube	muscle
36	chr18:12839600-12852000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr18:12839600-12854800	Weak transcription	Fetal Intestine Small	intestine
38	chr18:12839600-12855200	Weak transcription	Fetal Intestine Large	intestine
39	chr18:12839600-12857200	Weak transcription	Aorta	Aorta
40	chr18:12839600-12858800	Weak transcription	Adipose Nuclei	Adipose
41	chr18:12839600-12861200	Weak transcription	Brain Hippocampus Middle	brain
42	chr18:12839600-12862600	Weak transcription	HSMM	muscle
43	chr18:12839800-12842600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr18:12839800-12853400	Weak transcription	HepG2	liver
45	chr18:12840000-12848400	Weak transcription	HMEC	breast
46	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
47	chr18:12840200-12842600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr18:12840200-12842800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr18:12840200-12843800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr18:12840200-12851800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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