Variant report

Variant	rs12962340
Chromosome Location	chr18:12272923-12272924
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12271533..12274633-chr18:12277025..12281374,4	K562	blood:
2	chr18:12271750..12274682-chr18:12275072..12276921,2	K562	blood:
3	chr18:12271756..12273282-chr18:13725344..13726895,2	K562	blood:
4	chr18:12271574..12273371-chr18:12275461..12278516,4	MCF-7	breast:
5	chr18:12270328..12273534-chr18:12306877..12309950,3	K562	blood:
6	chr18:12270340..12273321-chr18:12306765..12308912,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction
ENSG00000177150	Chromatin interaction
ENSG00000101654	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11080562	0.84[EUR][1000 genomes]
rs11661656	0.83[EUR][1000 genomes]
rs12966610	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35460481	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7230089	0.84[EUR][1000 genomes]
rs7245001	0.84[EUR][1000 genomes]
rs7505021	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12272000-12277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:12272000-12278200	Weak transcription	Colonic Mucosa	Colon
3	chr18:12272200-12273000	Enhancers	Primary B cells from peripheral blood	blood
4	chr18:12272200-12273200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:12272200-12273600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr18:12272200-12273600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:12272200-12273800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr18:12272200-12274000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr18:12272200-12274000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr18:12272200-12276600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:12272200-12276600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr18:12272200-12276600	Weak transcription	Fetal Muscle Leg	muscle
13	chr18:12272200-12276600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:12272200-12276600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr18:12272200-12277000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr18:12272200-12277400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:12272200-12277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:12272200-12277400	Weak transcription	HSMMtube	muscle
19	chr18:12272200-12277800	Weak transcription	HMEC	breast
20	chr18:12272200-12278000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr18:12272200-12278000	Weak transcription	NHLF	lung
22	chr18:12272200-12278000	Weak transcription	Osteobl	bone
23	chr18:12272200-12278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr18:12272200-12278200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:12272200-12278200	Weak transcription	HSMM	muscle
26	chr18:12272200-12278400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr18:12272200-12278600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:12272400-12273200	Weak transcription	Adipose Nuclei	Adipose
29	chr18:12272400-12273400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr18:12272400-12276600	Weak transcription	Placenta	Placenta
31	chr18:12272400-12277400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:12272400-12277400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:12272600-12273000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr18:12272600-12274000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr18:12272800-12278200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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