Variant report

Variant	rs12090074
Chromosome Location	chr1:84660611-84660612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
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]
rs12092953	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:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84640400-84665000	Weak transcription	NH-A	brain
2	chr1:84646400-84662600	Weak transcription	Colonic Mucosa	Colon
3	chr1:84650600-84662400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:84652200-84675000	Weak transcription	Pancreas	Pancrea
5	chr1:84652400-84689800	Weak transcription	Aorta	Aorta
6	chr1:84653400-84674800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:84654800-84661000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:84654800-84661200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:84655000-84661200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr1:84657200-84665400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:84657400-84662400	Weak transcription	HSMM	muscle
12	chr1:84657400-84664800	Weak transcription	Brain Angular Gyrus	brain
13	chr1:84657400-84665000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:84657600-84708000	Weak transcription	Left Ventricle	heart
15	chr1:84657800-84665400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:84658400-84667600	Weak transcription	NHDF-Ad	bronchial
17	chr1:84658600-84665200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:84658800-84660800	Strong transcription	Fetal Brain Male	brain
19	chr1:84659000-84661600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:84659000-84662200	Weak transcription	Adipose Nuclei	Adipose
21	chr1:84659000-84662400	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:84659000-84662400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:84659000-84663800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:84659000-84666600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:84659000-84672000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:84659000-84674600	Weak transcription	Osteobl	bone
27	chr1:84659000-84685000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:84659000-84700600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:84659000-84700800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:84659200-84662800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:84659200-84677000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:84659200-84688400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:84659400-84661200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:84659400-84661200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:84659400-84661200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:84659400-84661600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:84659400-84662200	Weak transcription	Fetal Kidney	kidney
38	chr1:84659400-84662800	Weak transcription	Brain Anterior Caudate	brain
39	chr1:84659400-84663000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:84659400-84663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:84659400-84663600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:84659400-84666400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:84659400-84666600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:84659400-84668000	Strong transcription	Fetal Thymus	thymus
45	chr1:84659400-84670400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:84659400-84672000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:84659400-84675200	Strong transcription	Dnd41	blood
48	chr1:84659400-84677200	Weak transcription	Psoas Muscle	Psoas
49	chr1:84659400-84685400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:84659600-84661000	Strong transcription	Brain Substantia Nigra	brain

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