Variant report

Variant	rs12754750
Chromosome Location	chr1:246887594-246887595
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246858802..246860634-chr1:246887473..246889819,2	MCF-7	breast:
2	chr1:246853163..246855096-chr1:246886538..246888986,3	MCF-7	breast:
3	chr1:246852890..246853392-chr1:246887551..246888079,2	K562	blood:
4	chr1:246853196..246855742-chr1:246886661..246889205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12117425	0.83[EUR][1000 genomes]
rs12132175	0.84[EUR][1000 genomes]
rs12737081	0.83[EUR][1000 genomes]
rs12741733	0.83[EUR][1000 genomes]
rs34112967	0.83[EUR][1000 genomes]
rs34116211	0.83[EUR][1000 genomes]
rs34413394	0.83[EUR][1000 genomes]
rs34732921	0.83[EUR][1000 genomes]
rs35588974	0.83[EUR][1000 genomes]
rs35778672	0.83[EUR][1000 genomes]
rs61855391	0.83[EUR][1000 genomes]
rs7550798	0.83[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	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246886600-246888000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:246886600-246888400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:246886600-246888400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:246886600-246888400	Active TSS	NHLF	lung
5	chr1:246886600-246888600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:246886600-246889000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:246886800-246887600	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr1:246886800-246887800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:246886800-246887800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:246886800-246887800	Active TSS	HepG2	liver
11	chr1:246886800-246888000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:246886800-246888000	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:246886800-246888200	Active TSS	Primary T cells from cord blood	blood
14	chr1:246886800-246888200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:246886800-246888200	Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr1:246886800-246888400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:246886800-246888400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:246886800-246888400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:246886800-246888400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:246886800-246888400	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr1:246886800-246888400	Active TSS	Aorta	Aorta
22	chr1:246886800-246888400	Active TSS	Brain Anterior Caudate	brain
23	chr1:246886800-246888400	Active TSS	Brain Cingulate Gyrus	brain
24	chr1:246886800-246888400	Active TSS	Brain Germinal Matrix	brain
25	chr1:246886800-246888400	Active TSS	Stomach Smooth Muscle	stomach
26	chr1:246886800-246888400	Active TSS	A549	lung
27	chr1:246886800-246888400	Active TSS	GM12878-XiMat	blood
28	chr1:246886800-246888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:246886800-246888600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:246886800-246888600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:246886800-246888600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:246886800-246888600	Active TSS	Brain Angular Gyrus	brain
33	chr1:246886800-246888600	Active TSS	Colon Smooth Muscle	Colon
34	chr1:246886800-246888600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:246886800-246888600	Active TSS	Fetal Intestine Large	intestine
36	chr1:246886800-246888600	Active TSS	Fetal Intestine Small	intestine
37	chr1:246886800-246888600	Active TSS	Fetal Stomach	stomach
38	chr1:246886800-246888600	Active TSS	Right Ventricle	heart
39	chr1:246886800-246888800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:246886800-246888800	Active TSS	Brain Substantia Nigra	brain
41	chr1:246886800-246888800	Active TSS	Fetal Brain Female	brain
42	chr1:246886800-246888800	Active TSS	HSMM	muscle
43	chr1:246886800-246888800	Active TSS	K562	blood
44	chr1:246886800-246889000	Active TSS	Duodenum Mucosa	Duodenum
45	chr1:246886800-246889000	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:246886800-246889200	Active TSS	NHDF-Ad	bronchial
47	chr1:246887000-246887800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:246887000-246887800	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr1:246887000-246887800	Active TSS	NHEK	skin
50	chr1:246887000-246888000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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