Variant report

Variant	rs12404994
Chromosome Location	chr1:154740864-154740865
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10908438	0.80[ASN][1000 genomes]
rs11264257	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11584403	0.87[ASN][1000 genomes]
rs11589471	0.83[ASN][1000 genomes]
rs12047201	0.82[ASN][1000 genomes]
rs12134335	0.91[AFR][1000 genomes]
rs4845391	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56995760	0.83[ASN][1000 genomes]
rs60161870	0.83[ASN][1000 genomes]
rs6426929	0.80[ASN][1000 genomes]
rs6666341	0.82[ASN][1000 genomes]
rs7532286	0.80[ASN][1000 genomes]
rs7547552	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
3	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr1:154733400-154743800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:154733400-154744200	Weak transcription	Spleen	Spleen
3	chr1:154733400-154746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:154738400-154742000	Enhancers	Fetal Muscle Trunk	muscle
5	chr1:154739000-154741000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:154739000-154741400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:154739400-154741200	Enhancers	HSMMtube	muscle
8	chr1:154739400-154741600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:154739400-154741600	Enhancers	Placenta	Placenta
10	chr1:154739400-154741800	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:154739400-154741800	Genic enhancers	Fetal Stomach	stomach
12	chr1:154739600-154741200	Enhancers	Brain Hippocampus Middle	brain
13	chr1:154739600-154741400	Enhancers	Brain Anterior Caudate	brain
14	chr1:154739600-154741600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:154739600-154741800	Enhancers	Colon Smooth Muscle	Colon
16	chr1:154739600-154742200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr1:154739800-154741200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:154739800-154741400	Enhancers	Brain Substantia Nigra	brain
19	chr1:154739800-154741400	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:154739800-154741400	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr1:154739800-154742000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:154740000-154741400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:154740000-154741600	Strong transcription	GM12878-XiMat	blood
24	chr1:154740200-154741000	Weak transcription	Left Ventricle	heart
25	chr1:154740200-154741000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
26	chr1:154740200-154741400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:154740200-154744800	Weak transcription	Colonic Mucosa	Colon
28	chr1:154740400-154741000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr1:154740400-154744000	Weak transcription	Fetal Brain Female	brain
30	chr1:154740400-154746000	Weak transcription	Brain Germinal Matrix	brain
31	chr1:154740400-154747600	Weak transcription	Fetal Brain Male	brain
32	chr1:154740600-154741600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr1:154740800-154746000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:154740800-154746200	Weak transcription	Brain Angular Gyrus	brain
35	chr1:154740800-154764000	Weak transcription	Right Ventricle	heart

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