Variant report

Variant	rs17004734
Chromosome Location	chr21:46521458-46521459
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	chr21:46493552..46495288-chr21:46521401..46524653,4	MCF-7	breast:
3	chr21:46514549..46517055-chr21:46520921..46524159,3	MCF-7	breast:
4	chr21:46493580..46496236-chr21:46521352..46523890,2	MCF-7	breast:
5	chr21:46515956..46522233-chr21:46528087..46531013,7	K562	blood:
6	chr21:46492354..46499042-chr21:46517406..46531809,25	K562	blood:

Variant related genes	Relation type
ENSG00000197381	Chromatin interaction
ENSG00000268805	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10222166	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs12482868	0.97[ASN][1000 genomes]
rs12482952	0.93[ASN][1000 genomes]
rs12482954	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12483020	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12483115	0.84[ASN][1000 genomes]
rs12483279	0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12483312	0.96[ASN][1000 genomes]
rs12483758	0.96[ASN][1000 genomes]
rs12627065	0.89[JPT][hapmap]
rs12627151	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]
rs1556316	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1556318	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs1556319	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs17004739	0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17004743	0.81[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap]
rs17004748	0.81[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap]
rs2838774	0.90[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2838776	0.84[CHB][hapmap];0.82[JPT][hapmap];0.99[ASN][1000 genomes]
rs2838786	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2838789	0.91[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838792	0.92[JPT][hapmap]
rs2838801	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2838802	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2838809	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs2838810	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs2838811	0.89[JPT][hapmap]
rs2838812	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2838816	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs3178603	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs367228	0.90[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs372173	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs372549	0.92[JPT][hapmap]
rs3746976	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3788154	0.96[ASN][1000 genomes]
rs3788155	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3788156	0.90[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3788163	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3788164	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs3788169	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]
rs3788170	0.81[CHB][hapmap]
rs3788171	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs3788181	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs386528	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs390504	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs406551	0.83[CEU][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs412626	0.83[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs412666	0.83[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.82[AMR][1000 genomes]
rs421643	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs423726	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs428870	0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs431529	0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs431666	0.82[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs431775	0.81[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs437286	0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs439884	0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs442380	0.83[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs447656	0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs454052	0.83[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs6518215	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs6518216	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs6518218	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7275205	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7275931	0.93[ASN][1000 genomes]
rs7277143	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7279808	0.90[JPT][hapmap]
rs7281718	0.96[ASN][1000 genomes]
rs7283317	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7283619	0.99[ASN][1000 genomes]
rs731248	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8127577	0.91[ASN][1000 genomes]
rs8129934	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8130862	0.91[JPT][hapmap]
rs8132454	0.91[ASN][1000 genomes]
rs8132752	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8134889	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs870145	0.90[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs870350	0.99[ASN][1000 genomes]
rs870351	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17004734	C21orf122	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 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	chr21:46509400-46524000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr21:46512000-46521600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr21:46512200-46521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr21:46512200-46522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr21:46512200-46525600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:46513400-46521600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:46513600-46522200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr21:46513600-46522400	Weak transcription	Brain Hippocampus Middle	brain
13	chr21:46513600-46522600	Weak transcription	Aorta	Aorta
14	chr21:46513600-46522600	Weak transcription	Brain Anterior Caudate	brain
15	chr21:46513800-46522000	Weak transcription	Stomach Mucosa	stomach
16	chr21:46514200-46525000	Enhancers	Right Ventricle	heart
17	chr21:46514600-46522600	Weak transcription	Fetal Thymus	thymus
18	chr21:46514800-46522200	Weak transcription	Primary T cells from cord blood	blood
19	chr21:46514800-46523800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr21:46515000-46522200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46515200-46521800	Weak transcription	Pancreas	Pancrea
22	chr21:46515200-46522000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr21:46515400-46522000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr21:46515600-46522400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr21:46516200-46522200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr21:46516200-46524000	Weak transcription	Gastric	stomach
27	chr21:46516400-46521600	Weak transcription	HMEC	breast
28	chr21:46516400-46525600	Weak transcription	K562	blood
29	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr21:46516600-46521600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:46516600-46522000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr21:46516600-46522600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:46516600-46522600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr21:46517400-46523800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr21:46518200-46522600	Weak transcription	Esophagus	oesophagus
36	chr21:46518600-46523600	Weak transcription	Placenta	Placenta
37	chr21:46519000-46522200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr21:46519200-46521600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr21:46519200-46521600	Weak transcription	HSMM	muscle
40	chr21:46519200-46521800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:46519200-46521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr21:46519200-46522000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr21:46519200-46522000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr21:46519200-46522000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr21:46519400-46526800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr21:46519800-46522000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr21:46519800-46522200	Weak transcription	HSMMtube	muscle
48	chr21:46519800-46522600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr21:46520000-46522200	Weak transcription	Fetal Heart	heart
50	chr21:46520200-46521800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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