Variant report

Variant	rs56995760
Chromosome Location	chr1:154744141-154744142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154743914..154746256-chr1:154842086..154843825,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143603	Chromatin interaction

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

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

rs_ID	r²[population]
rs10908439	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264257	0.87[ASN][1000 genomes]
rs11584403	0.96[ASN][1000 genomes]
rs11589471	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808053	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047201	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12404994	0.83[ASN][1000 genomes]
rs4845391	0.82[ASN][1000 genomes]
rs55829123	0.83[EUR][1000 genomes]
rs60161870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666341	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72700247	0.84[EUR][1000 genomes]
rs7547552	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154733400-154744200	Weak transcription	Spleen	Spleen
2	chr1:154733400-154746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154740200-154744800	Weak transcription	Colonic Mucosa	Colon
4	chr1:154740400-154746000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:154740400-154747600	Weak transcription	Fetal Brain Male	brain
6	chr1:154740800-154746000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:154740800-154746200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:154740800-154764000	Weak transcription	Right Ventricle	heart
9	chr1:154741000-154744200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:154741200-154745600	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:154741400-154745200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:154741400-154745600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:154741400-154745600	Weak transcription	Thymus	Thymus
14	chr1:154741400-154746200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:154741400-154746600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:154741800-154745800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:154741800-154746000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:154742000-154744200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:154742000-154744800	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:154742200-154751400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:154742800-154744200	Weak transcription	Fetal Stomach	stomach
22	chr1:154743200-154744800	Strong transcription	GM12878-XiMat	blood
23	chr1:154743600-154745800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:154743800-154746000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:154744000-154744400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:154744000-154744800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:154744000-154744800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:154744000-154744800	Strong transcription	Fetal Brain Female	brain
29	chr1:154744000-154745000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:154744000-154745400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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