Variant report

Variant	rs538957
Chromosome Location	chr5:80312876-80312877
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	chr13:51532795..51533745-chr5:80312236..80312930,2	MCF-7	breast:
2	chr5:80312638..80314887-chr5:80409746..80411334,2	K562	blood:

Variant related genes	Relation type
ENSG00000249772	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11750489	1.00[YRI][hapmap]
rs481785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs483970	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[MEX][hapmap]
rs497522	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs499090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs501544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509741	0.87[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs516660	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517880	1.00[YRI][hapmap]
rs521812	0.80[ASN][1000 genomes]
rs527116	0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs527506	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs533308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535083	0.80[ASN][1000 genomes]
rs539809	0.86[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs546746	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555979	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs564459	0.84[ASN][1000 genomes]
rs565476	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs565834	0.81[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs569262	0.86[CEU][hapmap];0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs570858	0.86[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs6453538	0.85[CEU][hapmap]

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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4897	chr5:80284196-80330223	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538957	ZCCHC9	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80300000-80313000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:80300400-80316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:80300400-80318400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80303000-80318200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:80303800-80314400	Weak transcription	HepG2	liver
6	chr5:80305000-80315000	Weak transcription	Left Ventricle	heart
7	chr5:80305200-80318200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:80309800-80317000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:80311000-80317400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:80311600-80313800	Enhancers	Primary T cells from cord blood	blood
11	chr5:80311600-80315000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr5:80311600-80323800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr5:80311600-80325400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:80311800-80313000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:80311800-80314400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:80311800-80314400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:80312000-80313400	Enhancers	Brain Substantia Nigra	brain
18	chr5:80312000-80315800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:80312200-80313000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:80312200-80313200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:80312200-80316200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:80312200-80316400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:80312200-80323600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:80312800-80313000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:80312800-80313200	Enhancers	Brain Anterior Caudate	brain
26	chr5:80312800-80313200	Enhancers	Fetal Stomach	stomach
27	chr5:80312800-80313400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:80312800-80313400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:80312800-80313400	Enhancers	Brain Angular Gyrus	brain
30	chr5:80312800-80313400	Enhancers	Fetal Lung	lung
31	chr5:80312800-80313800	Enhancers	Brain Hippocampus Middle	brain
32	chr5:80312800-80314200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:80312800-80314400	Enhancers	Brain Cingulate Gyrus	brain
34	chr5:80312800-80315400	Enhancers	Primary T cells fromperipheralblood	blood
35	chr5:80312800-80320000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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