Variant report

Variant	rs17004733
Chromosome Location	chr21:46520840-46520841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46519046..46522635-chr21:46528087..46531462,4	K562	blood:
2	chr21:46421527..46423886-chr21:46518850..46521282,2	MCF-7	breast:
3	chr21:46515956..46522233-chr21:46528087..46531013,7	K562	blood:
4	chr21:46492354..46499042-chr21:46517406..46531809,25	K562	blood:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2104812	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs2236702	0.84[CEU][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap]
rs3788152	0.92[CEU][hapmap]
rs387097	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs7275998	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729895	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs872768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3359090	chr21:46519949-46522497	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17004733	KRTAP10-8	cis	multi-tissue	Pritchard
rs17004733	C21orf2	cis	multi-tissue	Pritchard
rs17004733	C21orf122	cis	multi-tissue	Pritchard
rs17004733	ICOSLG	cis	multi-tissue	Pritchard
rs17004733	UBE2G2	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 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	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:46513600-46522200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr21:46513600-46522400	Weak transcription	Brain Hippocampus Middle	brain
14	chr21:46513600-46522600	Weak transcription	Aorta	Aorta
15	chr21:46513600-46522600	Weak transcription	Brain Anterior Caudate	brain
16	chr21:46513800-46522000	Weak transcription	Stomach Mucosa	stomach
17	chr21:46514200-46525000	Enhancers	Right Ventricle	heart
18	chr21:46514600-46522600	Weak transcription	Fetal Thymus	thymus
19	chr21:46514800-46522200	Weak transcription	Primary T cells from cord blood	blood
20	chr21:46514800-46523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr21:46515000-46522200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr21:46515200-46521800	Weak transcription	Pancreas	Pancrea
23	chr21:46515200-46522000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr21:46515400-46522000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr21:46515600-46522400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr21:46516200-46522200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr21:46516200-46524000	Weak transcription	Gastric	stomach
28	chr21:46516400-46521600	Weak transcription	HMEC	breast
29	chr21:46516400-46525600	Weak transcription	K562	blood
30	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr21:46516600-46521600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:46516600-46522000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr21:46516600-46522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr21:46516600-46522600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr21:46517400-46523800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr21:46517600-46521400	Weak transcription	Adipose Nuclei	Adipose
37	chr21:46517600-46521400	Enhancers	Fetal Brain Male	brain
38	chr21:46518200-46522600	Weak transcription	Esophagus	oesophagus
39	chr21:46518600-46523600	Weak transcription	Placenta	Placenta
40	chr21:46518800-46521200	Weak transcription	Hela-S3	cervix
41	chr21:46519000-46522200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr21:46519200-46521600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr21:46519200-46521600	Weak transcription	HSMM	muscle
44	chr21:46519200-46521800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr21:46519200-46521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr21:46519200-46522000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr21:46519200-46522000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr21:46519200-46522000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr21:46519400-46526800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr21:46519800-46522000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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