Variant report

Variant	rs1556316
Chromosome Location	chr21:46550392-46550393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46358799..46362946-chr21:46546409..46551680,5	K562	blood:
2	chr21:46492924..46497122-chr21:46547379..46551295,4	MCF-7	breast:
3	chr21:46386181..46388411-chr21:46549880..46552492,2	MCF-7	breast:
4	chr21:46491911..46497737-chr21:46547142..46552694,13	K562	blood:
5	chr21:46544212..46547881-chr21:46548757..46552730,5	K562	blood:
6	chr21:46492248..46501057-chr21:46545477..46562980,48	K562	blood:
7	chr21:46530815..46533467-chr21:46549475..46551001,2	K562	blood:

Variant related genes	Relation type
ENSG00000183250	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10222166	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs12482868	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12482952	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12482954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483279	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483312	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12483758	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12627065	0.90[JPT][hapmap]
rs12627151	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1556318	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs1556319	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs17004734	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17004739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004743	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17004748	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838776	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838789	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2838792	0.93[JPT][hapmap]
rs2838801	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838802	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs2838809	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2838810	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs2838811	0.90[JPT][hapmap]
rs2838812	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs2838816	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3178603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs367228	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs372173	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs372549	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs3746976	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes]
rs3788154	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3788155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788164	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3788169	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs3788170	0.90[CHB][hapmap]
rs3788171	0.90[CHB][hapmap]
rs3788181	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs386528	0.93[JPT][hapmap]
rs390504	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs391834	0.85[ASN][1000 genomes]
rs406551	0.92[JPT][hapmap]
rs412626	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs412666	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs421643	0.93[JPT][hapmap]
rs423726	0.93[JPT][hapmap]
rs428870	0.92[JPT][hapmap]
rs431529	0.92[JPT][hapmap]
rs431666	0.93[JPT][hapmap]
rs431775	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs437286	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs439884	0.92[JPT][hapmap]
rs442380	0.92[JPT][hapmap]
rs447656	0.92[JPT][hapmap]
rs454052	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs6518215	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs6518216	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs6518218	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7275205	0.90[ASN][1000 genomes]
rs7275931	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7277143	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7279808	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs7281718	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7283317	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7283619	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs731248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127577	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8130862	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs8132454	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8132752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8134889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs870145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs870350	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs870351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	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
3	nsv522002	chr21:46542670-46551702	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 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	chr21:46532600-46552400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr21:46532600-46570600	Weak transcription	Dnd41	blood
6	chr21:46538800-46552200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr21:46541800-46552400	Weak transcription	Fetal Brain Male	brain
8	chr21:46542800-46551400	Weak transcription	Lung	lung
9	chr21:46544200-46558200	Weak transcription	HepG2	liver
10	chr21:46544200-46560400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:46544400-46552400	Weak transcription	Thymus	Thymus
12	chr21:46545000-46554800	Enhancers	Fetal Muscle Leg	muscle
13	chr21:46545200-46550400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr21:46545600-46553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr21:46546400-46551400	Enhancers	Fetal Heart	heart
16	chr21:46546600-46554600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr21:46546800-46552800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr21:46546800-46555200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr21:46547200-46552400	Weak transcription	Primary T cells from cord blood	blood
20	chr21:46547600-46551200	Enhancers	Primary B cells from cord blood	blood
21	chr21:46548200-46550400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:46548200-46553400	Enhancers	Colon Smooth Muscle	Colon
23	chr21:46548200-46553600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr21:46548400-46550400	Enhancers	HSMMtube	muscle
25	chr21:46548400-46550400	Enhancers	NHLF	lung
26	chr21:46548400-46551800	Enhancers	Rectal Smooth Muscle	rectum
27	chr21:46548600-46550400	Enhancers	Brain Hippocampus Middle	brain
28	chr21:46548600-46550400	Weak transcription	GM12878-XiMat	blood
29	chr21:46548600-46551400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr21:46548600-46551800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr21:46548600-46552200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr21:46548600-46552600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr21:46548600-46554000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr21:46548600-46554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr21:46548600-46571600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr21:46548800-46550400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr21:46548800-46550600	Enhancers	Stomach Mucosa	stomach
38	chr21:46548800-46551200	Weak transcription	Liver	Liver
39	chr21:46548800-46554800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:46548800-46558400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr21:46549000-46550400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr21:46549000-46551000	Enhancers	HMEC	breast
43	chr21:46549200-46550400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr21:46549200-46550400	Enhancers	Ovary	ovary
45	chr21:46549200-46550800	Enhancers	A549	lung
46	chr21:46549400-46550400	Enhancers	Colonic Mucosa	Colon
47	chr21:46549400-46550400	Enhancers	Fetal Lung	lung
48	chr21:46549400-46550400	Flanking Active TSS	Osteobl	bone
49	chr21:46549400-46550800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr21:46549400-46550800	Enhancers	Fetal Intestine Small	intestine

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