Variant report

Variant	rs12965889
Chromosome Location	chr18:12289151-12289152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12282293..12284100-chr18:12288664..12290381,2	MCF-7	breast:
2	chr18:12289075..12291340-chr18:12294128..12296061,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12326653	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12961753	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12965777	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4797665	0.94[YRI][hapmap]
rs7233146	0.91[ASN][1000 genomes]
rs7240908	0.88[ASN][1000 genomes]
rs8099469	0.82[AMR][1000 genomes]
rs9989524	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9989596	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12287200-12289200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr18:12287200-12289400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr18:12287400-12289400	Flanking Active TSS	NHEK	skin
4	chr18:12287600-12289200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr18:12287600-12289200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr18:12287600-12289200	Enhancers	Lung	lung
7	chr18:12287600-12289200	Active TSS	Right Atrium	heart
8	chr18:12287600-12289200	Flanking Active TSS	NH-A	brain
9	chr18:12287600-12289400	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr18:12287600-12289400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
11	chr18:12287800-12289400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
12	chr18:12288000-12289400	Flanking Active TSS	K562	blood
13	chr18:12288200-12289200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
14	chr18:12288200-12289200	Bivalent Enhancer	Fetal Intestine Large	intestine
15	chr18:12288200-12289200	Flanking Active TSS	Left Ventricle	heart
16	chr18:12288200-12289200	Flanking Active TSS	Osteobl	bone
17	chr18:12288200-12289400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr18:12288400-12289200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr18:12288400-12289200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr18:12288400-12289200	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr18:12288400-12289200	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr18:12288400-12289200	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr18:12288400-12289200	Flanking Active TSS	NHLF	lung
27	chr18:12288400-12289400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr18:12288400-12289400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12288400-12289400	Flanking Active TSS	HMEC	breast
30	chr18:12288400-12289400	Flanking Active TSS	HSMM	muscle
31	chr18:12288400-12289400	Flanking Active TSS	HSMMtube	muscle
32	chr18:12288400-12296200	Weak transcription	Spleen	Spleen
33	chr18:12288600-12289200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:12288600-12289200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr18:12288600-12289200	Bivalent Enhancer	Brain Anterior Caudate	brain
36	chr18:12288600-12289200	Bivalent Enhancer	Brain Hippocampus Middle	brain
37	chr18:12288600-12289200	Bivalent Enhancer	Fetal Lung	lung
38	chr18:12288600-12289200	Bivalent Enhancer	Placenta	Placenta
39	chr18:12288600-12289200	Enhancers	Ovary	ovary
40	chr18:12288600-12289200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr18:12288600-12289400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr18:12288600-12289400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr18:12288600-12289400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr18:12288600-12289400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
45	chr18:12288600-12291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr18:12288600-12291800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:12288800-12289200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12288800-12289200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr18:12288800-12289200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr18:12288800-12289200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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