Variant report

Variant	rs4402715
Chromosome Location	chr2:20828195-20828196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
2	chr2:20665586..20667484-chr2:20827548..20829987,2	MCF-7	breast:
3	chr2:20826020..20829529-chr2:20830645..20833872,5	MCF-7	breast:
4	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
5	chr2:20816763..20821100-chr2:20824834..20828532,5	K562	blood:
6	chr2:20827354..20828915-chr2:20830990..20833952,3	K562	blood:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000228950	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10186292	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186814	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187254	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191266	0.98[ASN][1000 genomes]
rs10199441	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10432583	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1047169	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11096680	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11687806	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468175	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476211	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12710742	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998196	0.85[ASN][1000 genomes]
rs13022516	0.84[ASN][1000 genomes]
rs1529896	0.81[ASN][1000 genomes]
rs1865678	0.84[ASN][1000 genomes]
rs2033639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033640	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305457	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3732151	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796064	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666317	0.85[EUR][1000 genomes]
rs4666318	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666438	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666439	0.84[ASN][1000 genomes]
rs4666445	0.98[ASN][1000 genomes]
rs4666446	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666447	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60569709	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62122089	0.85[ASN][1000 genomes]
rs6737130	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750073	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7423811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875672	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:113 , 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	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
9	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
10	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
14	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:20818800-20833600	Weak transcription	A549	lung
16	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:20819800-20834200	Weak transcription	Osteobl	bone
21	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:20821400-20831800	Weak transcription	NHEK	skin
24	chr2:20822000-20832600	Weak transcription	Hela-S3	cervix
25	chr2:20822200-20828800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:20823000-20833600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:20823000-20833600	Weak transcription	HSMMtube	muscle
28	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:20823200-20831800	Weak transcription	HMEC	breast
30	chr2:20823400-20834200	Weak transcription	Small Intestine	intestine
31	chr2:20824000-20833600	Strong transcription	Fetal Intestine Small	intestine
32	chr2:20824400-20828800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:20824400-20829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:20824600-20828600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:20824600-20828800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:20824600-20828800	Weak transcription	Brain Germinal Matrix	brain
37	chr2:20824600-20828800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:20824600-20829000	Weak transcription	Liver	Liver
39	chr2:20824600-20829000	Weak transcription	Fetal Lung	lung
40	chr2:20824600-20829200	Weak transcription	Fetal Brain Female	brain
41	chr2:20824600-20833600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:20824600-20834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:20824600-20834200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:20824600-20835000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:20824600-20837400	Weak transcription	Thymus	Thymus
46	chr2:20824600-20837800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr2:20824600-20839000	Weak transcription	Dnd41	blood
48	chr2:20824800-20828800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:20824800-20829200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:20824800-20829200	Weak transcription	Ovary	ovary

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