Variant report

Variant	rs400140
Chromosome Location	chr21:46535814-46535815
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	chr21:46535673-46535871	HepG2	liver:	n/a	chr21:46535784-46535793

No.	Distal block	Cell Line	Cell type
1	chr21:46534608..46536339-chr21:46539154..46541485,2	K562	blood:
2	chr21:46493538..46495350-chr21:46535458..46537231,2	K562	blood:
3	chr21:46493305..46495041-chr21:46533530..46536007,3	K562	blood:

Variant related genes	Relation type
ENSG00000267857	TF binding region
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2150438	0.80[CHB][hapmap]
rs2838763	0.80[CHB][hapmap]
rs2838771	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs373687	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes]
rs414743	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs419322	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs4819027	0.90[ASN][1000 genomes]
rs7282639	0.80[CHB][hapmap]
rs8130074	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9977825	0.85[AMR][1000 genomes];0.81[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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr21:46522600-46538600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:46523000-46548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr21:46526400-46549400	Weak transcription	Brain Substantia Nigra	brain
5	chr21:46526800-46536400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:46528800-46536600	Genic enhancers	HSMM	muscle
7	chr21:46528800-46537200	Enhancers	Left Ventricle	heart
8	chr21:46529200-46536600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:46529200-46537400	Weak transcription	Ovary	ovary
10	chr21:46529200-46538400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:46529400-46540400	Weak transcription	Gastric	stomach
12	chr21:46529400-46549400	Weak transcription	Esophagus	oesophagus
13	chr21:46529600-46537200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr21:46530400-46538600	Weak transcription	Fetal Kidney	kidney
16	chr21:46530400-46548400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr21:46531000-46537000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr21:46531200-46536400	Enhancers	Primary B cells from cord blood	blood
21	chr21:46531200-46538800	Enhancers	Primary B cells from peripheral blood	blood
22	chr21:46531200-46542400	Weak transcription	Thymus	Thymus
23	chr21:46531400-46549600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr21:46531800-46541800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr21:46531800-46548200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr21:46531800-46548200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr21:46531800-46548600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr21:46532600-46537800	Weak transcription	Primary T cells from cord blood	blood
29	chr21:46532600-46542000	Weak transcription	Fetal Thymus	thymus
30	chr21:46532600-46545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:46532600-46552400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr21:46532600-46570600	Weak transcription	Dnd41	blood
33	chr21:46532800-46536400	Enhancers	HSMMtube	muscle
34	chr21:46532800-46537000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr21:46532800-46540200	Weak transcription	Adipose Nuclei	Adipose
36	chr21:46532800-46548400	Weak transcription	Osteobl	bone
37	chr21:46533000-46540200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr21:46533600-46536600	Strong transcription	Hela-S3	cervix
39	chr21:46533800-46542400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:46534000-46543000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr21:46534200-46539200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr21:46534600-46537400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr21:46534600-46540400	Weak transcription	Fetal Brain Male	brain
44	chr21:46534800-46536000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:46534800-46544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr21:46534800-46545200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr21:46534800-46549600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr21:46535000-46536000	Enhancers	HMEC	breast
49	chr21:46535000-46536200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr21:46535000-46536600	Weak transcription	HUVEC	blood vessel

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