Variant report

Variant	rs1038564
Chromosome Location	chr2:172920423-172920424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172915241..172921806-chr2:172947514..172951783,14	MCF-7	breast:
2	chr2:172919420..172922156-chr2:172937386..172939240,3	MCF-7	breast:
3	chr2:172920303..172928510-chr2:172947424..172952310,9	K562	blood:
4	chr2:172915456..172917874-chr2:172919849..172921461,2	MCF-7	breast:
5	chr2:172915810..172921925-chr2:172947139..172950933,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10167594	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10171214	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10203462	0.92[ASN][1000 genomes]
rs10209911	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497377	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10930503	1.00[CHB][hapmap];1.00[JPT][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]
rs11892858	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12052482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12616766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403822	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1344393	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17581610	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs17615589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17615607	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357323	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796058	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs56923699	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57656367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751078	0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs705870	0.82[JPT][hapmap]
rs73976544	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976547	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs788164	0.91[JPT][hapmap]
rs9973494	0.90[AMR][1000 genomes]
rs9973784	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911000-172930000	Weak transcription	Primary T cells from cord blood	blood
2	chr2:172911200-172947200	Weak transcription	HSMM	muscle
3	chr2:172914000-172937000	Weak transcription	Pancreas	Pancrea
4	chr2:172917200-172927200	Weak transcription	Left Ventricle	heart
5	chr2:172917200-172927200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:172917400-172927000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:172917400-172934800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:172917800-172925800	Weak transcription	Fetal Lung	lung
9	chr2:172917800-172927800	Weak transcription	Ovary	ovary
10	chr2:172917800-172932000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:172918000-172920800	Weak transcription	K562	blood
13	chr2:172918000-172930400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:172918600-172927200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
17	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:172918800-172926200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:172919000-172921400	Weak transcription	HepG2	liver
20	chr2:172920000-172925400	Weak transcription	Brain Germinal Matrix	brain

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