Variant report

Variant	rs12092953
Chromosome Location	chr1:84656229-84656230
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11163912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070688	1.00[AMR][1000 genomes]
rs12075034	1.00[AMR][1000 genomes]
rs12077806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082320	1.00[AMR][1000 genomes]
rs12086972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17131229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3729864	1.00[AMR][1000 genomes]
rs3729865	1.00[AMR][1000 genomes]
rs41301154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41301156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41301160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41301162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv871731	chr1:84597396-84658591	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv871656	chr1:84601048-84693671	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997601	chr1:84609346-84672859	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1005225	chr1:84609871-84667950	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1002537	chr1:84611207-84658450	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv999772	chr1:84611207-84667218	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1013911	chr1:84619164-84667950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv871375	chr1:84622793-84678418	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv871538	chr1:84633116-84717983	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking 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 miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv1011105	chr1:84638386-84674276	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1837139	chr1:84649799-84670584	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84635000-84656400	Weak transcription	Fetal Heart	heart
2	chr1:84640000-84656600	Weak transcription	Left Ventricle	heart
3	chr1:84640000-84658800	Weak transcription	Fetal Brain Male	brain
4	chr1:84640200-84656400	Weak transcription	HSMMtube	muscle
5	chr1:84640200-84658600	Weak transcription	Osteobl	bone
6	chr1:84640400-84656600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:84640400-84658200	Weak transcription	NHDF-Ad	bronchial
8	chr1:84640400-84658400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:84640400-84665000	Weak transcription	NH-A	brain
10	chr1:84641200-84658600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:84643200-84656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:84643400-84656600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:84643400-84656600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:84644000-84656400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:84644400-84658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:84646400-84662600	Weak transcription	Colonic Mucosa	Colon
17	chr1:84647000-84656400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:84647000-84656600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:84647200-84656800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:84647400-84658800	Strong transcription	Fetal Thymus	thymus
21	chr1:84648600-84656400	Weak transcription	Brain Substantia Nigra	brain
22	chr1:84649400-84659800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:84649600-84658200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:84650000-84658800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:84650600-84658600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:84650600-84662400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:84650800-84658000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:84650800-84658600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:84652200-84658600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:84652200-84675000	Weak transcription	Pancreas	Pancrea
31	chr1:84652400-84656600	Weak transcription	Ovary	ovary
32	chr1:84652400-84689800	Weak transcription	Aorta	Aorta
33	chr1:84652600-84656400	Weak transcription	HSMM	muscle
34	chr1:84652600-84656600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:84652600-84657200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:84652600-84658400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:84652600-84658600	Weak transcription	Fetal Stomach	stomach
38	chr1:84653000-84656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:84653000-84656400	Weak transcription	Adipose Nuclei	Adipose
40	chr1:84653000-84656600	Weak transcription	Thymus	Thymus
41	chr1:84653200-84656400	Weak transcription	Fetal Brain Female	brain
42	chr1:84653200-84656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:84653200-84656600	Weak transcription	Liver	Liver
44	chr1:84653200-84656800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:84653200-84657000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:84653200-84658400	Weak transcription	HUVEC	blood vessel
47	chr1:84653400-84674800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:84653600-84656400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:84653600-84656600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:84654000-84659400	ZNF genes & repeats	Dnd41	blood

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