Variant report

Variant	rs2838780
Chromosome Location	chr21:46518433-46518434
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr21:46518390-46519300	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr21:46518351-46518538	K562	blood:	n/a	n/a
3	ZNF143	chr21:46518403-46518512	K562	blood:	n/a	n/a
4	POLR2A	chr21:46518340-46519049	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr21:46518419-46519340	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46495351..46497648-chr21:46516468..46519256,2	MCF-7	breast:
2	chr21:46513400..46515958-chr21:46516220..46519288,3	MCF-7	breast:
3	chr21:46493347..46495290-chr21:46517134..46518749,2	MCF-7	breast:
4	chr21:46510275..46513095-chr21:46517504..46519501,2	MCF-7	breast:
5	chr21:46515956..46522233-chr21:46528087..46531013,7	K562	blood:
6	chr21:46492354..46499042-chr21:46517406..46531809,25	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268805	TF binding region
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000268805	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11908769	0.89[AFR][1000 genomes]
rs11911694	0.89[AFR][1000 genomes]
rs17004737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004740	0.89[AFR][1000 genomes]
rs17004746	0.89[AFR][1000 genomes]
rs2032253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838772	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2838775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877003	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3171490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373249	1.00[ASN][1000 genomes]
rs375621	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs387536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs406923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs407157	1.00[ASN][1000 genomes]
rs412431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs420499	1.00[CEU][hapmap]
rs422205	0.93[ASN][1000 genomes]
rs423892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs425176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs437833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs444789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs451550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73230653	1.00[AMR][1000 genomes]
rs73230658	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73230662	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73230667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230679	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230680	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8133767	1.00[CHB][hapmap];1.00[JPT][hapmap]

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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
2	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
4	chr21:46506600-46521400	Weak transcription	NHEK	skin
5	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
7	chr21:46511800-46520200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr21:46512800-46520400	Enhancers	Fetal Muscle Leg	muscle
13	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr21:46513400-46518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr21:46513600-46518600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr21:46513600-46519800	Enhancers	Left Ventricle	heart
18	chr21:46513600-46520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr21:46513600-46522200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr21:46513600-46522400	Weak transcription	Brain Hippocampus Middle	brain
21	chr21:46513600-46522600	Weak transcription	Aorta	Aorta
22	chr21:46513600-46522600	Weak transcription	Brain Anterior Caudate	brain
23	chr21:46513800-46520400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr21:46513800-46522000	Weak transcription	Stomach Mucosa	stomach
25	chr21:46514200-46518800	Enhancers	Spleen	Spleen
26	chr21:46514200-46525000	Enhancers	Right Ventricle	heart
27	chr21:46514400-46518600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:46514600-46522600	Weak transcription	Fetal Thymus	thymus
29	chr21:46514800-46519200	Genic enhancers	HSMM	muscle
30	chr21:46514800-46522200	Weak transcription	Primary T cells from cord blood	blood
31	chr21:46514800-46523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr21:46515000-46522200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr21:46515200-46518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr21:46515200-46521800	Weak transcription	Pancreas	Pancrea
35	chr21:46515200-46522000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr21:46515400-46522000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr21:46515600-46522400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr21:46516200-46522200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:46516200-46524000	Weak transcription	Gastric	stomach
40	chr21:46516400-46519000	Weak transcription	Psoas Muscle	Psoas
41	chr21:46516400-46519800	Enhancers	Fetal Muscle Trunk	muscle
42	chr21:46516400-46520400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr21:46516400-46521600	Weak transcription	HMEC	breast
44	chr21:46516400-46525600	Weak transcription	K562	blood
45	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr21:46516600-46520200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr21:46516600-46520800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:46516600-46521600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr21:46516600-46522000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr21:46516600-46522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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