Variant report

Variant	rs624724
Chromosome Location	chr21:46287456-46287457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46249596..46252365-chr21:46286693..46288889,2	K562	blood:
2	chr21:46272684..46279612-chr21:46286573..46290125,9	K562	blood:
3	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
4	chr21:46247392..46250185-chr21:46286804..46289409,3	MCF-7	breast:
5	chr21:46231789..46243695-chr21:46286819..46295664,23	MCF-7	breast:
6	chr21:46279667..46283456-chr21:46286447..46289465,4	K562	blood:
7	chr21:46286677..46288930-chr6:170126669..170128404,2	K562	blood:
8	chr21:46222162..46224765-chr21:46287052..46289071,2	K562	blood:
9	chr21:46237355..46239033-chr21:46286989..46289637,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITGB2-1	chr21:46286389-46288992	ENSG00000250713

No data

Variant related genes	Relation type
ENSG00000236519	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000184900	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11312	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs170960	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs173093	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs180318	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs235276	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs235280	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs235282	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs235298	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs235302	0.92[EUR][1000 genomes]
rs235315	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235319	0.85[EUR][1000 genomes]
rs235371	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235377	0.91[EUR][1000 genomes]
rs28568877	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs410038	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs440555	0.93[EUR][1000 genomes]
rs596566	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs84193	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs624724	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr21:46279400-46288400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
5	chr21:46279800-46287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:46283400-46288800	Strong transcription	NHEK	skin
7	chr21:46284000-46288400	Genic enhancers	Spleen	Spleen
8	chr21:46284000-46289000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr21:46284600-46287600	Genic enhancers	Fetal Intestine Large	intestine
10	chr21:46284600-46287800	Genic enhancers	Gastric	stomach
11	chr21:46284800-46288600	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr21:46285000-46288400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:46285000-46291600	Enhancers	Primary hematopoietic stem cells	blood
14	chr21:46285000-46291800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:46285200-46287800	Genic enhancers	Fetal Intestine Small	intestine
16	chr21:46285200-46287800	Genic enhancers	Stomach Smooth Muscle	stomach
17	chr21:46285200-46287800	Genic enhancers	Dnd41	blood
18	chr21:46285200-46287800	Genic enhancers	NHLF	lung
19	chr21:46285200-46288600	Genic enhancers	Right Ventricle	heart
20	chr21:46285200-46288800	Genic enhancers	Osteobl	bone
21	chr21:46285200-46289000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr21:46285200-46289200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr21:46285200-46290000	Genic enhancers	Fetal Thymus	thymus
24	chr21:46285200-46290800	Enhancers	Right Atrium	heart
25	chr21:46285200-46291600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr21:46285400-46287600	Genic enhancers	Rectal Smooth Muscle	rectum
27	chr21:46285400-46287600	Genic enhancers	Thymus	Thymus
28	chr21:46285400-46287600	Genic enhancers	HMEC	breast
29	chr21:46285400-46288600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr21:46285400-46289000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:46285400-46291600	Enhancers	Left Ventricle	heart
32	chr21:46285600-46288600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr21:46285600-46289400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr21:46285600-46291600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:46285600-46291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr21:46285600-46292200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr21:46285800-46288000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:46285800-46288400	Genic enhancers	Fetal Muscle Leg	muscle
39	chr21:46285800-46289000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr21:46285800-46289200	Enhancers	Brain Angular Gyrus	brain
41	chr21:46285800-46289400	Enhancers	Brain Substantia Nigra	brain
42	chr21:46285800-46290000	Enhancers	Brain Anterior Caudate	brain
43	chr21:46286000-46287800	Genic enhancers	Primary T cells from cord blood	blood
44	chr21:46286000-46288000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr21:46286000-46288000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr21:46286000-46289000	Genic enhancers	K562	blood
47	chr21:46286000-46289600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr21:46286000-46289600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:46286000-46289600	Enhancers	Colon Smooth Muscle	Colon
50	chr21:46286000-46290600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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