Variant report

Variant	rs926579
Chromosome Location	chr1:210590153-210590154
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	chr1:210590026..210592841-chr1:211432035..211434761,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117625	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10863826	0.82[ASN][1000 genomes]
rs11119486	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119489	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12136541	0.82[YRI][hapmap]
rs12738703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357587	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3753226	0.87[ASW][hapmap]
rs4601592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4845019	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4845021	0.83[ASW][hapmap]
rs4845025	0.83[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs57153723	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6682398	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518269	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7538194	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[AFR][1000 genomes];0.93[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	esv2756883	chr1:210579523-210620779	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv2758995	chr1:210579523-210620779	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs926579	C1orf107	cis	cerebellum	SCAN
rs926579	NEK2	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210567400-210617200	Weak transcription	Left Ventricle	heart
2	chr1:210570200-210594000	Weak transcription	Fetal Lung	lung
3	chr1:210571200-210592400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:210571400-210591400	Weak transcription	Ovary	ovary
5	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:210573600-210592400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:210573800-210592200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:210573800-210594400	Weak transcription	Spleen	Spleen
9	chr1:210574400-210592200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:210574400-210594400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:210574400-210595200	Weak transcription	Right Ventricle	heart
12	chr1:210577400-210591600	Weak transcription	Thymus	Thymus
13	chr1:210581200-210592400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:210583400-210592400	Weak transcription	Liver	Liver
15	chr1:210584400-210591600	Weak transcription	Esophagus	oesophagus
16	chr1:210585200-210593600	Weak transcription	Fetal Stomach	stomach
17	chr1:210586400-210610800	Weak transcription	Aorta	Aorta
18	chr1:210587600-210591400	Enhancers	HSMMtube	muscle
19	chr1:210589200-210591000	Enhancers	Fetal Brain Male	brain
20	chr1:210589400-210590200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:210589400-210590200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:210589400-210590200	Enhancers	Fetal Brain Female	brain
23	chr1:210589400-210592800	Enhancers	HSMM	muscle
24	chr1:210589600-210590200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:210589600-210590200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr1:210589600-210591000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:210589600-210592600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:210590000-210590200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:210590000-210592400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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