Variant report

Variant	rs729895
Chromosome Location	chr21:46515421-46515422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46515041..46517271-chr21:46546796..46549469,2	K562	blood:
2	chr21:46494313..46497302-chr21:46514232..46516454,3	MCF-7	breast:
3	chr21:46493165..46495720-chr21:46513762..46518212,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17004733	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]
rs2104812	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs2236702	0.84[CEU][hapmap];0.83[JPT][hapmap];0.87[YRI][hapmap]
rs3788152	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs387097	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs7275998	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73907241	0.81[EUR][1000 genomes]
rs872768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs729895	C21orf122	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46496600-46516200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr21:46499000-46522200	Weak transcription	NHDF-Ad	bronchial
3	chr21:46500000-46522200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr21:46502000-46516000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr21:46503000-46522200	Weak transcription	Brain Angular Gyrus	brain
6	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr21:46503200-46516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr21:46506600-46521400	Weak transcription	NHEK	skin
9	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr21:46510200-46515600	Weak transcription	K562	blood
11	chr21:46510600-46519200	Enhancers	Primary B cells from peripheral blood	blood
12	chr21:46511800-46515600	Weak transcription	HMEC	breast
13	chr21:46511800-46520200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr21:46512200-46515800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:46512200-46518000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr21:46512800-46516200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr21:46512800-46520400	Enhancers	Fetal Muscle Leg	muscle
22	chr21:46513000-46515600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr21:46513000-46516600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:46513000-46516600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr21:46513000-46516600	Enhancers	Fetal Heart	heart
26	chr21:46513000-46517600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr21:46513400-46515600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:46513400-46518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr21:46513600-46515800	Weak transcription	Fetal Lung	lung
32	chr21:46513600-46516000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr21:46513600-46516200	Weak transcription	HSMMtube	muscle
34	chr21:46513600-46517200	Weak transcription	Fetal Stomach	stomach
35	chr21:46513600-46517600	Enhancers	Adipose Nuclei	Adipose
36	chr21:46513600-46518600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr21:46513600-46519800	Enhancers	Left Ventricle	heart
38	chr21:46513600-46520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr21:46513600-46522200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr21:46513600-46522400	Weak transcription	Brain Hippocampus Middle	brain
41	chr21:46513600-46522600	Weak transcription	Aorta	Aorta
42	chr21:46513600-46522600	Weak transcription	Brain Anterior Caudate	brain
43	chr21:46513800-46516000	Weak transcription	Psoas Muscle	Psoas
44	chr21:46513800-46516200	Enhancers	Stomach Smooth Muscle	stomach
45	chr21:46513800-46520400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr21:46513800-46522000	Weak transcription	Stomach Mucosa	stomach
47	chr21:46514200-46516200	Enhancers	Fetal Brain Female	brain
48	chr21:46514200-46516400	Enhancers	Lung	lung
49	chr21:46514200-46516400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr21:46514200-46516600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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