Variant report

Variant	rs17797571
Chromosome Location	chr4:56805661-56805662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:56804922..56810078-chr4:56811128..56817037,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174799	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1072799	1.00[ASN][1000 genomes]
rs11727702	1.00[ASN][1000 genomes]
rs11729456	1.00[ASN][1000 genomes]
rs11734942	1.00[ASN][1000 genomes]
rs17086086	1.00[CEU][hapmap]
rs17086132	1.00[ASN][1000 genomes]
rs17086150	1.00[ASN][1000 genomes]
rs17086186	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086254	1.00[ASN][1000 genomes]
rs17728804	1.00[ASN][1000 genomes]
rs17740755	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742000	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17742722	1.00[ASN][1000 genomes]
rs17743071	1.00[ASN][1000 genomes]
rs17797113	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797407	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797595	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17798452	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17798872	1.00[ASN][1000 genomes]
rs2899046	1.00[ASN][1000 genomes]
rs2899053	1.00[ASN][1000 genomes]
rs34179097	1.00[ASN][1000 genomes]
rs34184679	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34650834	1.00[ASN][1000 genomes]
rs35143702	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41279543	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280345	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56026480	1.00[ASN][1000 genomes]
rs61753870	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814812	1.00[ASN][1000 genomes]
rs6817717	1.00[ASN][1000 genomes]
rs6833480	1.00[ASN][1000 genomes]
rs6845953	1.00[ASN][1000 genomes]
rs6848009	1.00[ASN][1000 genomes]
rs73238359	1.00[ASN][1000 genomes]
rs73238365	1.00[ASN][1000 genomes]
rs73238367	1.00[ASN][1000 genomes]
rs73238368	1.00[ASN][1000 genomes]
rs73238369	1.00[ASN][1000 genomes]
rs73238370	1.00[ASN][1000 genomes]
rs73238371	1.00[ASN][1000 genomes]
rs73238372	1.00[ASN][1000 genomes]
rs73238373	1.00[ASN][1000 genomes]
rs73238377	1.00[ASN][1000 genomes]
rs73238379	1.00[ASN][1000 genomes]
rs73238380	1.00[ASN][1000 genomes]
rs73238381	1.00[ASN][1000 genomes]
rs73238382	1.00[ASN][1000 genomes]
rs73238383	1.00[ASN][1000 genomes]
rs73238384	1.00[ASN][1000 genomes]
rs73238387	1.00[ASN][1000 genomes]
rs73238390	1.00[ASN][1000 genomes]
rs73238395	1.00[ASN][1000 genomes]
rs73238397	1.00[ASN][1000 genomes]
rs73238398	1.00[ASN][1000 genomes]
rs73238399	1.00[ASN][1000 genomes]
rs73238400	1.00[ASN][1000 genomes]
rs748013	1.00[ASN][1000 genomes]
rs7657912	1.00[ASN][1000 genomes]
rs7669903	1.00[ASN][1000 genomes]
rs7675287	1.00[ASN][1000 genomes]
rs7690739	1.00[ASN][1000 genomes]
rs7698100	1.00[ASN][1000 genomes]
rs9994601	1.00[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	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv879025	chr4:56742205-56808607	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv964348	chr4:56782802-56815653	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56803400-56806600	ZNF genes & repeats	Primary T cells from cord blood	blood
2	chr4:56803600-56807000	Strong transcription	HUVEC	blood vessel
3	chr4:56803800-56806400	Weak transcription	Lung	lung
4	chr4:56803800-56813400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:56804200-56806400	Enhancers	Primary hematopoietic stem cells	blood
6	chr4:56804200-56812800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:56804400-56805800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:56804400-56805800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:56804400-56805800	ZNF genes & repeats	Left Ventricle	heart
10	chr4:56804400-56807600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr4:56804400-56812600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr4:56804800-56806400	Enhancers	Fetal Intestine Small	intestine
13	chr4:56804800-56806800	Enhancers	Fetal Intestine Large	intestine
14	chr4:56805000-56805800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:56805000-56806000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr4:56805000-56807600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:56805200-56806000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:56805200-56811000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:56805200-56812600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:56805200-56814600	Weak transcription	Spleen	Spleen
21	chr4:56805400-56805800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr4:56805400-56805800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr4:56805400-56805800	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr4:56805400-56806400	Enhancers	HepG2	liver
25	chr4:56805600-56805800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:56805600-56805800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:56805600-56807000	Strong transcription	Primary B cells from cord blood	blood

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