Variant report

Variant	rs56243158
Chromosome Location	chr7:66529501-66529502
allele	C/T
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	CBX3	chr7:66529399-66529765	K562	blood:	n/a	n/a
2	SETDB1	chr7:66529318-66529760	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
TYW1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10256861	0.81[AFR][1000 genomes]
rs10282273	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10950060	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760318	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12531934	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12537557	0.94[ASN][1000 genomes]
rs17144722	0.84[EUR][1000 genomes]
rs2421287	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28760321	0.83[EUR][1000 genomes]
rs34512474	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34787423	0.80[ASN][1000 genomes]
rs35644973	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3962073	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4717347	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4718452	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs55958146	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60356903	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60666480	0.92[AFR][1000 genomes]
rs6962222	0.83[AFR][1000 genomes]
rs7794497	0.87[EUR][1000 genomes]
rs7801361	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7809810	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9654849	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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv981515	chr7:66477535-66532313	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs56243158	TYW1	cis	Esophagus Mucosa	GTEx
rs56243158	TYW1	cis	Muscle Skeletal	GTEx
rs56243158	TYW1	cis	Nerve Tibial	GTEx
rs56243158	GS1-124K5.4	cis	Nerve Tibial	GTEx
rs56243158	TYW1	cis	Heart Left Ventricle	GTEx
rs56243158	TYW1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66483400-66551200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:66483600-66534400	Weak transcription	Aorta	Aorta
3	chr7:66486400-66531600	Weak transcription	Ovary	ovary
4	chr7:66487000-66576600	Weak transcription	Gastric	stomach
5	chr7:66495000-66532200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:66495200-66538000	Weak transcription	Brain Germinal Matrix	brain
7	chr7:66495200-66539400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:66495200-66597200	Weak transcription	Right Ventricle	heart
9	chr7:66495400-66529600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:66495400-66531800	Weak transcription	Fetal Kidney	kidney
11	chr7:66495400-66533200	Weak transcription	Thymus	Thymus
12	chr7:66495400-66534400	Weak transcription	Spleen	Spleen
13	chr7:66495600-66532200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:66495600-66533200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:66495600-66547400	Weak transcription	Pancreas	Pancrea
16	chr7:66498600-66534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:66498600-66549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:66501000-66540000	Weak transcription	Psoas Muscle	Psoas
19	chr7:66502400-66534400	Weak transcription	Lung	lung
20	chr7:66502400-66549600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:66506600-66534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:66508000-66532200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr7:66508000-66533400	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:66508800-66533400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:66508800-66533800	Weak transcription	Hela-S3	cervix
26	chr7:66508800-66537600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:66508800-66538000	Weak transcription	A549	lung
28	chr7:66508800-66590400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:66509000-66531200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:66509000-66531200	Weak transcription	Osteobl	bone
31	chr7:66509000-66533200	Weak transcription	HSMM	muscle
32	chr7:66509000-66538000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:66509000-66539600	Weak transcription	HMEC	breast
34	chr7:66509400-66533000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:66509400-66536600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:66510800-66532000	Weak transcription	K562	blood
37	chr7:66511200-66537600	Weak transcription	Brain Substantia Nigra	brain
38	chr7:66511400-66539800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:66512000-66531600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:66512400-66535000	Weak transcription	Colonic Mucosa	Colon
41	chr7:66512400-66540600	Weak transcription	HepG2	liver
42	chr7:66515600-66537600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr7:66515600-66538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:66516200-66534400	Weak transcription	Placenta	Placenta
45	chr7:66516400-66533000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:66516400-66534600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:66516400-66551600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr7:66516600-66533200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:66516800-66532000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:66516800-66533200	Weak transcription	Left Ventricle	heart

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