Variant report

Variant	rs372173
Chromosome Location	chr21:46552998-46552999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46377934..46380318-chr21:46552188..46553755,2	K562	blood:
2	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
3	chr21:46532796..46535414-chr21:46551102..46553894,2	K562	blood:
4	chr21:46552512..46554278-chr21:46555488..46557400,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000267857	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000160256	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10222166	0.86[JPT][hapmap]
rs12482954	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12483020	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12483115	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12483279	0.92[JPT][hapmap]
rs12483312	0.80[ASN][1000 genomes]
rs12483758	0.80[ASN][1000 genomes]
rs12627065	0.82[JPT][hapmap]
rs12627151	0.85[JPT][hapmap]
rs1556316	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1556318	0.85[JPT][hapmap]
rs1556319	0.86[JPT][hapmap]
rs17004734	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs17004739	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17004743	0.85[JPT][hapmap]
rs17004748	0.85[JPT][hapmap]
rs2838774	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2838786	0.93[JPT][hapmap]
rs2838789	0.82[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2838792	0.86[JPT][hapmap]
rs2838801	0.86[JPT][hapmap]
rs2838802	0.86[JPT][hapmap]
rs2838809	0.85[JPT][hapmap]
rs2838810	0.85[JPT][hapmap]
rs2838811	0.82[JPT][hapmap]
rs2838812	0.86[JPT][hapmap]
rs2838816	0.85[JPT][hapmap]
rs3178603	0.93[JPT][hapmap]
rs367228	0.86[JPT][hapmap]
rs372549	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs3746976	0.86[JPT][hapmap]
rs3788154	0.80[ASN][1000 genomes]
rs3788155	0.93[JPT][hapmap]
rs3788156	0.92[JPT][hapmap]
rs3788163	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs3788164	0.92[JPT][hapmap]
rs3788169	0.85[JPT][hapmap]
rs3788181	0.86[JPT][hapmap]
rs386528	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs390504	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs391834	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406551	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs412626	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs412666	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs421643	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs423726	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs428870	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs431529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437286	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439884	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs442380	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs447656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs454052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518215	0.86[JPT][hapmap]
rs6518216	0.85[JPT][hapmap]
rs6518218	0.86[JPT][hapmap]
rs7275205	0.80[ASN][1000 genomes]
rs7277143	0.86[JPT][hapmap]
rs7279808	0.84[JPT][hapmap]
rs7283317	0.86[JPT][hapmap]
rs731248	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs8127577	0.85[ASN][1000 genomes]
rs8129934	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs8130862	0.85[JPT][hapmap]
rs8132454	0.85[ASN][1000 genomes]
rs8132752	0.93[JPT][hapmap]
rs8134889	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs870145	0.92[JPT][hapmap]
rs870351	0.93[JPT][hapmap]

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	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	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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46529800-46554800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr21:46530400-46554600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr21:46530800-46554600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr21:46532600-46570600	Weak transcription	Dnd41	blood
5	chr21:46544200-46558200	Weak transcription	HepG2	liver
6	chr21:46544200-46560400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr21:46545000-46554800	Enhancers	Fetal Muscle Leg	muscle
8	chr21:46545600-46553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr21:46546600-46554600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr21:46546800-46555200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr21:46548200-46553400	Enhancers	Colon Smooth Muscle	Colon
12	chr21:46548200-46553600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr21:46548600-46554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr21:46548600-46554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46548600-46571600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr21:46548800-46554800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr21:46548800-46558400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr21:46549800-46553000	Weak transcription	Esophagus	oesophagus
19	chr21:46549800-46554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr21:46549800-46554800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:46549800-46557200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr21:46549800-46559400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr21:46549800-46567600	Weak transcription	Gastric	stomach
24	chr21:46550000-46553400	Weak transcription	Brain Substantia Nigra	brain
25	chr21:46550000-46555800	Weak transcription	Aorta	Aorta
26	chr21:46550000-46567800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr21:46550200-46553800	Enhancers	Fetal Muscle Trunk	muscle
28	chr21:46550400-46571200	Weak transcription	Brain Germinal Matrix	brain
29	chr21:46550800-46553000	Enhancers	HUVEC	blood vessel
30	chr21:46550800-46553400	Enhancers	Adipose Nuclei	Adipose
31	chr21:46550800-46553600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr21:46550800-46554600	Weak transcription	Fetal Intestine Small	intestine
33	chr21:46550800-46563600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr21:46551000-46553600	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr21:46551000-46556400	Weak transcription	K562	blood
36	chr21:46551000-46562400	Weak transcription	HMEC	breast
37	chr21:46551200-46553400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr21:46551200-46553600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr21:46551200-46557000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr21:46551200-46557000	Strong transcription	Hela-S3	cervix
41	chr21:46551200-46557400	Weak transcription	Fetal Intestine Large	intestine
42	chr21:46551400-46553000	Weak transcription	Fetal Heart	heart
43	chr21:46551400-46553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr21:46551400-46553800	Enhancers	Psoas Muscle	Psoas
45	chr21:46551400-46555000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr21:46551400-46567400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr21:46551600-46553000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr21:46551600-46553000	Weak transcription	NHLF	lung
49	chr21:46551600-46554800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr21:46551600-46557200	Weak transcription	Brain Inferior Temporal Lobe	brain

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