Variant report

Variant	rs1041404
Chromosome Location	chr21:16424867-16424868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16422646..16426145-chr21:16428439..16434126,5	K562	blood:
2	chr21:16423927..16426073-chr21:16428028..16429939,3	K562	blood:
3	chr21:16424737..16426720-chr21:16531523..16533319,2	MCF-7	breast:
4	chr21:16423642..16425341-chr21:16436698..16438268,2	K562	blood:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1997577	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2142216	0.85[ASN][1000 genomes]
rs2223041	0.83[ASW][hapmap];0.85[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs2403873	0.95[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2403874	0.87[AFR][1000 genomes]
rs2823003	0.81[JPT][hapmap]
rs2823017	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.85[MKK][hapmap];0.98[ASN][1000 genomes]
rs2823022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2823027	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823029	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4356736	0.86[ASN][1000 genomes]
rs7280064	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs8132398	0.94[ASW][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs8133012	0.83[ASN][1000 genomes]
rs8133792	0.84[ASN][1000 genomes]
rs9982976	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060151	chr21:16295713-16435497	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv544378	chr21:16295713-16435497	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv834048	chr21:16324481-16489570	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv587050	chr21:16413682-16462268	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1059303	chr21:16423727-16466112	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv544379	chr21:16423727-16466112	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16401600-16426400	Weak transcription	HUVEC	blood vessel
2	chr21:16407400-16425600	Weak transcription	NHDF-Ad	bronchial
3	chr21:16407400-16431200	Weak transcription	NHEK	skin
4	chr21:16408600-16425800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr21:16410400-16426400	Weak transcription	HMEC	breast
6	chr21:16414400-16427200	Weak transcription	Aorta	Aorta
7	chr21:16415200-16431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:16415400-16427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:16415400-16429600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr21:16416400-16427000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:16419600-16427200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:16420400-16434800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:16421600-16425000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr21:16421800-16426600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr21:16422000-16427800	Enhancers	Colon Smooth Muscle	Colon
16	chr21:16422400-16425000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr21:16422400-16425200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr21:16422400-16426000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr21:16422400-16426000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr21:16422400-16426200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr21:16422600-16425000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr21:16422600-16425000	Enhancers	Fetal Kidney	kidney
23	chr21:16422600-16425200	Enhancers	Brain Angular Gyrus	brain
24	chr21:16422600-16426200	Enhancers	Brain Substantia Nigra	brain
25	chr21:16422600-16427000	Enhancers	HepG2	liver
26	chr21:16422800-16425200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr21:16422800-16427400	Enhancers	Brain Cingulate Gyrus	brain
28	chr21:16422800-16427600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr21:16422800-16435200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr21:16423000-16425000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr21:16423000-16425000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:16423000-16425000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr21:16423000-16425000	Enhancers	Primary B cells from peripheral blood	blood
34	chr21:16423000-16425000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr21:16423000-16425000	Enhancers	Psoas Muscle	Psoas
36	chr21:16423000-16425000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr21:16423000-16425200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr21:16423000-16425800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr21:16423000-16427800	Enhancers	Dnd41	blood
40	chr21:16423200-16425000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr21:16423200-16425000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr21:16423200-16425800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr21:16423200-16427600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr21:16423200-16429200	Enhancers	Brain Hippocampus Middle	brain
45	chr21:16423400-16425000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr21:16423400-16426000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr21:16423400-16426200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr21:16423600-16425000	Active TSS	Colonic Mucosa	Colon
49	chr21:16423600-16426000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr21:16423600-16426200	Enhancers	HUES48 Cell Line	embryonic stem cell

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