Variant report

Variant	rs57494499
Chromosome Location	chr2:20826512-20826513
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:20826460-20826610	GM12866	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20798603..20801119-chr2:20825014..20826613,2	K562	blood:
2	chr2:20826217..20828028-chr2:20848423..20850444,2	K562	blood:
3	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
4	chr2:20826020..20829529-chr2:20830645..20833872,5	MCF-7	breast:
5	chr2:20647196..20649386-chr2:20825674..20827981,2	K562	blood:
6	chr2:20672997..20675403-chr2:20825825..20827538,2	MCF-7	breast:
7	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
8	chr2:20816763..20821100-chr2:20824834..20828532,5	K562	blood:
9	chr2:20826367..20828028-chr2:20848944..20850812,2	K562	blood:
10	chr2:20818868..20821100-chr2:20824834..20827973,3	K562	blood:

No data

Variant related genes	Relation type
HS1BP3	TF binding region
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10176721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10200826	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10201427	1.00[EUR][1000 genomes]
rs10203073	1.00[EUR][1000 genomes]
rs11893093	1.00[EUR][1000 genomes]
rs1437408	1.00[EUR][1000 genomes]
rs16988071	1.00[EUR][1000 genomes]
rs1866043	1.00[EUR][1000 genomes]
rs28488411	0.85[AMR][1000 genomes]
rs28529647	0.85[AMR][1000 genomes]
rs28600892	0.85[AMR][1000 genomes]
rs28642817	0.85[AMR][1000 genomes]
rs340605	1.00[EUR][1000 genomes]
rs340608	1.00[EUR][1000 genomes]
rs548324	1.00[EUR][1000 genomes]
rs553687	1.00[EUR][1000 genomes]
rs55751815	0.85[AMR][1000 genomes]
rs56737091	1.00[EUR][1000 genomes]
rs571566	1.00[EUR][1000 genomes]
rs57524662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs582107	1.00[EUR][1000 genomes]
rs58590712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58696000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59300971	0.85[AMR][1000 genomes]
rs59771803	0.85[AMR][1000 genomes]
rs59882809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60283906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61478003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs642152	1.00[EUR][1000 genomes]
rs648568	1.00[EUR][1000 genomes]
rs662193	1.00[EUR][1000 genomes]
rs6736533	1.00[EUR][1000 genomes]
rs6759981	1.00[EUR][1000 genomes]
rs73224614	1.00[EUR][1000 genomes]
rs73235054	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73235060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235079	1.00[EUR][1000 genomes]
rs73235100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237122	0.91[AFR][1000 genomes]
rs73237135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237147	1.00[EUR][1000 genomes]
rs73919913	0.85[AMR][1000 genomes]
rs73919915	0.85[AMR][1000 genomes]
rs73919918	0.85[AMR][1000 genomes]
rs73919920	0.85[AMR][1000 genomes]
rs73919921	0.85[AMR][1000 genomes]
rs73919922	0.85[AMR][1000 genomes]
rs73919924	0.85[AMR][1000 genomes]
rs7564684	0.85[AMR][1000 genomes]
rs7574045	0.85[AMR][1000 genomes]
rs7574289	0.85[AMR][1000 genomes]
rs7601273	0.85[AMR][1000 genomes]
rs839914	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription 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	24 gene(s)	inside rSNPs	diseases
5	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
9	nsv999269	chr2:20824833-20869372	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20817200-20826600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
11	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
12	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
16	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20818800-20833600	Weak transcription	A549	lung
18	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:20819200-20827000	Strong transcription	Primary T cells from cord blood	blood
21	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:20819800-20826800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:20819800-20834200	Weak transcription	Osteobl	bone
26	chr2:20820600-20827000	Genic enhancers	Right Ventricle	heart
27	chr2:20820600-20827200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:20821000-20826800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:20821400-20831800	Weak transcription	NHEK	skin
32	chr2:20821600-20826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:20822000-20832600	Weak transcription	Hela-S3	cervix
34	chr2:20822200-20828800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20822400-20826600	Strong transcription	Placenta	Placenta
36	chr2:20823000-20833600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:20823000-20833600	Weak transcription	HSMMtube	muscle
38	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:20823200-20826600	Strong transcription	Fetal Intestine Large	intestine
40	chr2:20823200-20831800	Weak transcription	HMEC	breast
41	chr2:20823400-20826800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:20823400-20834200	Weak transcription	Small Intestine	intestine
43	chr2:20824000-20833600	Strong transcription	Fetal Intestine Small	intestine
44	chr2:20824200-20827000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:20824200-20827200	Weak transcription	Fetal Heart	heart
46	chr2:20824400-20826800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:20824400-20827200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:20824400-20827800	Enhancers	Left Ventricle	heart
49	chr2:20824400-20828800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:20824400-20829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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