Variant report

Variant	rs788171
Chromosome Location	chr2:172921832-172921833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:1104912..1105605-chr2:172921758..172922343,2	MCF-7	breast:
2	chr2:172361064..172363062-chr2:172920609..172922964,2	K562	blood:
3	chr2:172921135..172923645-chr2:172924728..172927557,3	K562	blood:
4	chr2:172903155..172905695-chr2:172921268..172923071,2	K562	blood:
5	chr2:172919420..172922156-chr2:172937386..172939240,3	MCF-7	breast:
6	chr2:172920303..172928510-chr2:172947424..172952310,9	K562	blood:
7	chr2:172920943..172924102-chr2:172929194..172933525,5	K562	blood:
8	chr2:172915810..172921925-chr2:172947139..172950933,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1008151	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12052246	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs12989560	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12991740	0.85[CEU][hapmap]
rs13015360	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13020884	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1965160	0.85[YRI][hapmap]
rs2129475	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34054371	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34737109	0.81[AMR][1000 genomes]
rs62183819	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6433323	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6725971	0.88[EUR][1000 genomes]
rs705870	0.86[AFR][1000 genomes]
rs788163	0.86[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs788166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs788170	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	0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs788171	MAP1D	cis	cerebellum	SCAN
rs788171	MAP1D	cis	parietal	SCAN
rs788171	SLC25A12	cis	parietal	SCAN
rs788171	AC068039.4	cis	Esophagus Muscularis	GTEx
rs788171	GORASP2	cis	cerebellum	SCAN
rs788171	SLC25A12	cis	cerebellum	SCAN
rs788171	AC068039.4	cis	Muscle Skeletal	GTEx
rs788171	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs788171	AC068039.4	cis	Thyroid	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	chr2:172918000-172930400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:172918000-172932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:172918600-172927200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:172918600-172935600	Weak transcription	Fetal Kidney	kidney
16	chr2:172918600-172935800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:172918800-172926200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:172920000-172925400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:172921200-172927000	Weak transcription	K562	blood
20	chr2:172921800-172937200	Weak transcription	HepG2	liver

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