Variant report

Variant	rs778521
Chromosome Location	chr3:23525625-23525626
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	JUND	chr3:23525445-23525679	HepG2	liver:	n/a	n/a
2	KAP1	chr3:23525391-23526291	HEK293	kidney:	n/a	n/a
3	KAP1	chr3:23525228-23525788	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000265645	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11708160	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs11711072	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11715841	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs11916411	0.86[GIH][hapmap]
rs12386394	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12715046	0.83[EUR][1000 genomes]
rs12715048	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13087861	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1353322	1.00[CEU][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1498809	0.89[GIH][hapmap]
rs1692622	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1692650	0.86[GIH][hapmap]
rs1695200	0.84[GIH][hapmap]
rs2036226	0.89[GIH][hapmap]
rs2055310	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs2133331	0.89[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs2173460	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs3104243	0.81[YRI][hapmap]
rs3111311	0.80[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3817002	0.89[CEU][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs4513393	0.84[GIH][hapmap]
rs4858069	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858074	1.00[CEU][hapmap];0.87[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs4858505	0.96[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858509	0.82[EUR][1000 genomes]
rs55797660	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58748418	0.91[EUR][1000 genomes]
rs60430884	0.90[EUR][1000 genomes]
rs60581845	0.94[ASN][1000 genomes]
rs60632986	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66649889	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763535	0.84[GIH][hapmap]
rs6770091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6776424	0.89[GIH][hapmap]
rs6795968	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6797907	0.89[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs6798153	0.86[CEU][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6798328	0.89[EUR][1000 genomes]
rs6805889	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs704533	0.84[GIH][hapmap]
rs704534	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs716456	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7612666	0.89[EUR][1000 genomes]
rs7613091	0.89[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7640308	0.84[GIH][hapmap]
rs778476	0.84[GIH][hapmap]
rs778480	0.84[GIH][hapmap]
rs778482	0.87[EUR][1000 genomes]
rs952134	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9815921	0.86[EUR][1000 genomes]
rs9820922	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9821419	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9830388	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs9830392	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836574	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9839738	0.88[CEU][hapmap];0.80[EUR][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	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs778521	THRB	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23512000-23527400	Weak transcription	Left Ventricle	heart
2	chr3:23513800-23527400	Weak transcription	Right Atrium	heart
3	chr3:23521000-23527600	Weak transcription	Right Ventricle	heart
4	chr3:23521000-23531800	Weak transcription	NHDF-Ad	bronchial
5	chr3:23521200-23527600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:23521600-23527400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:23521600-23532000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:23521800-23527400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:23521800-23527600	Weak transcription	Spleen	Spleen
10	chr3:23521800-23528600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:23522000-23525800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:23522000-23527400	Weak transcription	Thymus	Thymus
13	chr3:23522000-23527400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:23522000-23527800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:23522000-23531000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:23522000-23531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:23522200-23527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:23522200-23527400	Weak transcription	Primary B cells from cord blood	blood
19	chr3:23522200-23527600	Weak transcription	Fetal Thymus	thymus
20	chr3:23522200-23527800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:23522200-23528000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:23523000-23530800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:23523200-23536800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:23523400-23527200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:23523400-23527600	Weak transcription	Aorta	Aorta
26	chr3:23523400-23531000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:23523600-23527600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:23523600-23528000	Weak transcription	Brain Anterior Caudate	brain
29	chr3:23523600-23542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:23523800-23527400	Weak transcription	Fetal Lung	lung
31	chr3:23523800-23527400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:23524000-23534800	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:23524600-23526400	Enhancers	Adipose Nuclei	Adipose
34	chr3:23524800-23527600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:23524800-23531000	Weak transcription	Psoas Muscle	Psoas
36	chr3:23525200-23525800	Weak transcription	Primary T cells from cord blood	blood
37	chr3:23525200-23526000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:23525400-23527200	Weak transcription	Lung	lung
39	chr3:23525600-23526000	Enhancers	Fetal Heart	heart

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