Variant report

Variant	rs56780740
Chromosome Location	chr4:153083281-153083282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:153075644..153078430-chr4:153081633..153084131,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10030518	0.89[ASN][1000 genomes]
rs11099843	0.98[ASN][1000 genomes]
rs11721407	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11721782	0.89[ASN][1000 genomes]
rs11726930	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11727188	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11727862	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11732677	0.86[EUR][1000 genomes]
rs11733393	0.87[ASN][1000 genomes]
rs11733971	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736628	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11737156	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13112841	0.93[ASN][1000 genomes]
rs13131134	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17361391	0.86[EUR][1000 genomes]
rs2406622	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2406625	0.89[ASN][1000 genomes]
rs2897478	0.93[ASN][1000 genomes]
rs34069606	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34276148	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34909306	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35296212	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4557238	0.89[ASN][1000 genomes]
rs61226564	0.89[ASN][1000 genomes]
rs6535839	0.89[ASN][1000 genomes]
rs6535840	0.89[ASN][1000 genomes]
rs6823091	0.89[ASN][1000 genomes]
rs6833264	0.93[ASN][1000 genomes]
rs6837375	0.89[ASN][1000 genomes]
rs6843947	0.89[ASN][1000 genomes]
rs6848307	0.88[ASN][1000 genomes]
rs6858062	0.86[EUR][1000 genomes]
rs72736219	0.87[EUR][1000 genomes]
rs7662581	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7671283	0.94[ASN][1000 genomes]
rs7674458	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7675252	0.93[ASN][1000 genomes]
rs7675481	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7682931	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv880774	chr4:153035743-153121818	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56780740	RP11-18H21.1	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:153076400-153085600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:153078000-153085800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:153078000-153090600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:153080400-153084000	Weak transcription	Thymus	Thymus
5	chr4:153082000-153084800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:153082000-153085600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:153082200-153084000	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr4:153082400-153083400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr4:153082400-153084000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:153082400-153084000	Enhancers	HSMM	muscle
11	chr4:153082400-153084000	Enhancers	HSMMtube	muscle
12	chr4:153082600-153083600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:153082600-153083800	Enhancers	Adipose Nuclei	Adipose
14	chr4:153082600-153083800	Enhancers	HMEC	breast
15	chr4:153082600-153084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:153082600-153084000	Enhancers	Fetal Heart	heart
17	chr4:153082600-153084000	Enhancers	Osteobl	bone
18	chr4:153082800-153083400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:153082800-153083800	Enhancers	Brain Substantia Nigra	brain
20	chr4:153082800-153084000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:153083000-153083400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:153083000-153083400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:153083000-153083400	Enhancers	Brain Hippocampus Middle	brain
24	chr4:153083000-153083400	Weak transcription	Left Ventricle	heart
25	chr4:153083000-153083400	Enhancers	NH-A	brain
26	chr4:153083000-153083600	Weak transcription	Right Atrium	heart
27	chr4:153083000-153083800	Enhancers	HUVEC	blood vessel
28	chr4:153083200-153083600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:153083200-153083800	Enhancers	NHEK	skin
30	chr4:153083200-153084000	Enhancers	NHDF-Ad	bronchial

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