Variant report

Variant	rs17014866
Chromosome Location	chr1:209777675-209777676
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209751620..209753341-chr1:209777265..209778868,2	MCF-7	breast:
2	chr1:209776929..209778715-chr1:209779809..209782231,2	K562	blood:
3	chr1:209776183..209777954-chr1:209779787..209782159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008118	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10489339	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17014768	0.80[TSI][hapmap]
rs17014820	0.87[CHD][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs17014830	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs17014836	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs55967608	0.83[AFR][1000 genomes]
rs6658827	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs742253	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs7516885	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7536585	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs880782	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17014866	TMCC2	cis	parietal	SCAN
rs17014866	SLC30A1	cis	cerebellum	SCAN
rs17014866	C1orf97	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209764200-209780400	Weak transcription	Fetal Brain Male	brain
2	chr1:209764600-209791200	Weak transcription	Brain Anterior Caudate	brain
3	chr1:209769800-209781000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:209769800-209781200	Weak transcription	Spleen	Spleen
5	chr1:209771000-209780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:209771000-209787600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:209772200-209783000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:209774200-209780400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:209774800-209780400	Weak transcription	HMEC	breast
10	chr1:209775200-209778400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:209775600-209791400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:209775800-209780200	Weak transcription	NHEK	skin
13	chr1:209775800-209780400	Weak transcription	Osteobl	bone
14	chr1:209775800-209789800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:209776000-209778200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:209776000-209790200	Weak transcription	Brain Germinal Matrix	brain
17	chr1:209776000-209791000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:209776400-209780000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:209776600-209777800	Strong transcription	Ovary	ovary
20	chr1:209776600-209778400	Strong transcription	Brain Angular Gyrus	brain
21	chr1:209776800-209781200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:209777200-209778400	Enhancers	Fetal Heart	heart
23	chr1:209777600-209779600	Weak transcription	Fetal Lung	lung

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