Variant report

Variant	rs8128678
Chromosome Location	chr21:40497574-40497575
allele	A/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	RAD21	chr21:40497257-40498635	SK-N-SH	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
2	MAX	chr21:40497456-40498317	MCF-7	breast:	n/a	n/a
3	EGR1	chr21:40497483-40497838	K562	blood:	n/a	n/a
4	MYC	chr21:40497572-40497994	MCF-7	breast:	n/a	n/a
5	SMC3	chr21:40497459-40498802	SK-N-SH	brain:	n/a	chr21:40498057-40498071
6	EGR1	chr21:40497550-40497808	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40105498..40106623-chr21:40497124..40499103,7	MCF-7	breast:
2	chr21:40480387..40482431-chr21:40496618..40498616,2	MCF-7	breast:
3	chr21:40460586..40461779-chr21:40497559..40498490,3	MCF-7	breast:
4	chr21:40495398..40498019-chr21:40544324..40546654,2	K562	blood:
5	chr21:40493420..40495416-chr21:40496679..40498868,2	K562	blood:
6	chr21:40176932..40179361-chr21:40495597..40497932,3	MCF-7	breast:
7	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:
8	chr21:40496928..40499014-chr21:40502516..40504228,2	K562	blood:

Variant related genes	Relation type
RPL23AP12	TF binding region
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1013129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810383	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810384	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375073	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs431284	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442916	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454902	0.83[ASN][1000 genomes]
rs7283826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40486600-40497800	Weak transcription	Thymus	Thymus
2	chr21:40487200-40497600	Weak transcription	Colonic Mucosa	Colon
3	chr21:40487800-40497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr21:40493400-40497600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:40493800-40497600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr21:40494000-40497600	Weak transcription	Psoas Muscle	Psoas
7	chr21:40494000-40497600	Weak transcription	Spleen	Spleen
8	chr21:40494200-40497600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr21:40494200-40497600	Weak transcription	Esophagus	oesophagus
10	chr21:40494200-40497600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:40496000-40498400	Enhancers	Dnd41	blood
12	chr21:40496200-40498000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr21:40496200-40498000	Enhancers	Fetal Heart	heart
14	chr21:40496200-40498200	Enhancers	Stomach Smooth Muscle	stomach
15	chr21:40496200-40498400	Enhancers	Fetal Muscle Leg	muscle
16	chr21:40496200-40498400	Enhancers	NHDF-Ad	bronchial
17	chr21:40496200-40498600	Enhancers	HepG2	liver
18	chr21:40496200-40498800	Enhancers	Fetal Stomach	stomach
19	chr21:40496400-40497600	Enhancers	Rectal Smooth Muscle	rectum
20	chr21:40496400-40498000	Enhancers	Colon Smooth Muscle	Colon
21	chr21:40496400-40498000	Enhancers	Left Ventricle	heart
22	chr21:40496400-40498400	Enhancers	Fetal Lung	lung
23	chr21:40496400-40498800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr21:40496600-40497800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr21:40496600-40498000	Enhancers	Right Ventricle	heart
26	chr21:40496800-40497600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr21:40496800-40498000	Enhancers	Liver	Liver
28	chr21:40496800-40498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr21:40497000-40497600	Enhancers	Fetal Brain Male	brain
30	chr21:40497000-40497800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:40497000-40497800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr21:40497000-40498000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr21:40497000-40498000	Enhancers	Duodenum Mucosa	Duodenum
34	chr21:40497000-40498000	Enhancers	Right Atrium	heart
35	chr21:40497000-40498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr21:40497000-40498800	Enhancers	Lung	lung
37	chr21:40497400-40497600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr21:40497400-40498000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr21:40497400-40498000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr21:40497400-40498000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr21:40497400-40498000	Enhancers	NHLF	lung
42	chr21:40497400-40498400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr21:40497400-40498600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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