Variant report

Variant	rs12483065
Chromosome Location	chr21:16663614-16663615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:16569254..16574166-chr21:16662821..16666093,6	MCF-7	breast:
2	chr21:16662853..16665318-chr21:16789620..16791689,2	MCF-7	breast:
3	chr21:16663539..16666081-chr21:16712410..16715629,4	MCF-7	breast:
4	chr21:16575011..16578774-chr21:16661740..16665186,4	MCF-7	breast:
5	chr21:16663401..16665237-chr21:16852171..16854477,2	MCF-7	breast:
6	chr21:16581111..16587442-chr21:16661859..16666667,10	MCF-7	breast:
7	chr21:16570806..16572373-chr21:16663419..16665582,2	MCF-7	breast:
8	chr21:16436807..16439448-chr21:16663226..16666430,5	MCF-7	breast:
9	chr21:16662884..16665504-chr21:16853719..16855454,2	MCF-7	breast:
10	chr21:16656272..16660929-chr21:16661608..16666085,6	MCF-7	breast:
11	chr21:16577077..16584288-chr21:16662087..16667374,8	MCF-7	breast:
12	chr21:16235915..16238127-chr21:16662847..16665093,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction
ENSG00000236471	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10854377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13047829	0.81[EUR][1000 genomes]
rs13049627	0.88[ASN][1000 genomes]
rs1474513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2142237	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823207	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2823209	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823214	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823215	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823216	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823217	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2823219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823221	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2823224	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823225	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823226	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2823227	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823228	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2823229	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs722098	0.82[EUR][1000 genomes]
rs926133	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs982774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs982775	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1056659	chr21:16646531-16709391	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16659000-16665000	Weak transcription	HSMMtube	muscle
2	chr21:16662000-16670200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr21:16662400-16665800	Enhancers	Placenta	Placenta
4	chr21:16662400-16666000	Enhancers	Fetal Intestine Large	intestine
5	chr21:16662600-16666000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr21:16662600-16666400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr21:16662800-16664400	Weak transcription	Esophagus	oesophagus
8	chr21:16662800-16666200	Enhancers	Stomach Mucosa	stomach
9	chr21:16663000-16664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:16663000-16664000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr21:16663000-16664000	Weak transcription	Fetal Muscle Leg	muscle
12	chr21:16663000-16664000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr21:16663000-16666200	Enhancers	HMEC	breast
14	chr21:16663200-16663800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr21:16663200-16664000	Weak transcription	Colonic Mucosa	Colon
16	chr21:16663200-16664200	Enhancers	HepG2	liver
17	chr21:16663200-16665400	Weak transcription	Fetal Stomach	stomach
18	chr21:16663200-16665600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr21:16663200-16665800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr21:16663200-16665800	Enhancers	Fetal Intestine Small	intestine
21	chr21:16663200-16666200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr21:16663200-16674400	Weak transcription	Psoas Muscle	Psoas
23	chr21:16663400-16663800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr21:16663400-16663800	Weak transcription	Pancreas	Pancrea
25	chr21:16663400-16664200	Enhancers	Duodenum Mucosa	Duodenum
26	chr21:16663400-16664800	Weak transcription	Fetal Kidney	kidney
27	chr21:16663400-16665000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr21:16663400-16665200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr21:16663400-16665400	Weak transcription	K562	blood
30	chr21:16663400-16666000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr21:16663400-16676400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr21:16663600-16663800	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr21:16663600-16665000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr21:16663600-16665400	Enhancers	NHEK	skin
35	chr21:16663600-16666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr21:16663600-16666400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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