Variant report

Variant	rs56333646
Chromosome Location	chr7:128330140-128330141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr7:128330043-128330436	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:128325647..128328540-chr7:128329512..128331138,2	MCF-7	breast:
2	chr7:128320147..128324613-chr7:128325598..128330219,5	K562	blood:

Variant related genes	Relation type
IMP3P2	TF binding region
ENSG00000271344	TF binding region
ENSG00000205085	Chromatin interaction
ENSG00000270810	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1003241	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1109552	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11975784	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11977129	0.85[AMR][1000 genomes]
rs12670258	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12670271	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12671767	0.85[AMR][1000 genomes]
rs12672518	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12672529	0.85[AMR][1000 genomes]
rs12672576	0.85[AMR][1000 genomes]
rs12672608	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12674125	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1450874	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17169024	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17169357	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17169368	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17169609	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17533628	0.85[AMR][1000 genomes]
rs1839593	0.80[AMR][1000 genomes]
rs1839594	0.81[AMR][1000 genomes]
rs2290229	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4554406	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4728128	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4728130	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4731492	0.84[AMR][1000 genomes]
rs4731493	0.85[AMR][1000 genomes]
rs4731496	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4731497	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4731500	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4731501	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4731503	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4731504	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4731505	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4731506	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55978216	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56329625	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56916616	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57653865	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57886720	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61318942	0.85[AMR][1000 genomes]
rs61544090	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61738927	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62481938	0.84[AMR][1000 genomes]
rs62481939	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62481940	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62483364	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62483366	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62483368	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6467204	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6467206	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6467209	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6467210	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs67602452	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6945532	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6958788	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6969462	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6969554	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6973969	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6978887	0.85[AMR][1000 genomes]
rs73236020	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73236037	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7781695	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7797745	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv966738	chr7:128325654-128339129	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs56333646	RP11-274B21.1	cis	Thyroid	GTEx
rs56333646	RP11-274B21.4	cis	lung	GTEx
rs56333646	RP11-274B21.1	cis	Muscle Skeletal	GTEx
rs56333646	RP11-274B21.1	cis	Esophagus Muscularis	GTEx
rs56333646	RP11-274B21.4	cis	Nerve Tibial	GTEx
rs56333646	RP11-274B21.1	cis	Artery Aorta	GTEx
rs56333646	RP11-274B21.4	cis	Artery Tibial	GTEx
rs56333646	RP11-274B21.9	cis	Esophagus Mucosa	GTEx
rs56333646	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs56333646	RP11-274B21.1	cis	Artery Tibial	GTEx
rs56333646	RP11-274B21.2	cis	Artery Tibial	GTEx
rs56333646	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs56333646	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs56333646	RP11-274B21.1	cis	Whole Blood	GTEx
rs56333646	RP11-274B21.1	cis	lung	GTEx
rs56333646	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs56333646	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs56333646	RP11-274B21.4	cis	Thyroid	GTEx
rs56333646	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs56333646	RP11-274B21.2	cis	lung	GTEx
rs56333646	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs56333646	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs56333646	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs56333646	RP11-274B21.2	cis	Esophagus Muscularis	GTEx
rs56333646	RP11-274B21.4	cis	Whole Blood	GTEx
rs56333646	RP11-274B21.4	cis	Esophagus Muscularis	GTEx
rs56333646	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs56333646	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs56333646	RP11-274B21.4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128302400-128337200	Weak transcription	Gastric	stomach
2	chr7:128313400-128331200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:128313600-128337200	Weak transcription	Right Atrium	heart
4	chr7:128320200-128332000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:128320200-128337200	Weak transcription	NHLF	lung
6	chr7:128320400-128331000	Weak transcription	Brain Angular Gyrus	brain
7	chr7:128320400-128331000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:128321000-128332000	Weak transcription	Fetal Brain Male	brain
9	chr7:128322200-128333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:128323400-128337200	Weak transcription	Left Ventricle	heart
11	chr7:128324200-128337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:128324400-128330200	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:128324400-128330600	Weak transcription	Osteobl	bone
14	chr7:128324400-128337200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr7:128324600-128330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:128324800-128330800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:128325600-128333800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:128325600-128337000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:128325800-128330200	Weak transcription	Ovary	ovary
20	chr7:128326000-128330600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:128326000-128337200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr7:128326800-128331200	Weak transcription	Fetal Brain Female	brain
23	chr7:128328000-128330200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:128328000-128330800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:128328000-128331200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr7:128328000-128331600	Weak transcription	Aorta	Aorta
27	chr7:128328000-128332800	Weak transcription	Brain Anterior Caudate	brain
28	chr7:128328000-128333400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr7:128328000-128334000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:128328000-128334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:128328000-128337000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:128328000-128337200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:128328000-128337200	Weak transcription	HSMMtube	muscle
34	chr7:128328000-128337200	Weak transcription	NH-A	brain
35	chr7:128328200-128337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:128328800-128337200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:128329000-128337200	Weak transcription	HSMM	muscle
38	chr7:128329400-128333400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:128329400-128337200	Weak transcription	Pancreas	Pancrea
40	chr7:128329800-128331400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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