Variant report

Variant	rs788170
Chromosome Location	chr2:172919958-172919959
allele	C/T
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	chr2:172901921..172905424-chr2:172916575..172920187,5	MCF-7	breast:
3	chr2:172919420..172922156-chr2:172937386..172939240,3	MCF-7	breast:
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: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1008151	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12052246	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12989560	0.81[AMR][1000 genomes]
rs12991740	0.86[CEU][hapmap]
rs13015360	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13020884	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1965160	0.83[YRI][hapmap]
rs2129475	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34054371	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34737109	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62183819	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6433323	0.85[CEU][hapmap]
rs6725971	0.87[EUR][1000 genomes]
rs788163	0.96[YRI][hapmap]
rs788166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs788171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796839	0.91[EUR][1000 genomes];0.99[ASN][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs788170	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs788170	AC068039.4	cis	Thyroid	GTEx
rs788170	AC068039.4	cis	Esophagus Muscularis	GTEx
rs788170	AC068039.4	cis	Muscle Skeletal	GTEx

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	chr2:172919600-172920000	Enhancers	Brain Germinal Matrix	brain

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