Variant report

Variant	rs2066233
Chromosome Location	chr1:225618159-225618160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225616757..225618444-chr1:225653517..225655559,2	K562	blood:
2	chr1:225617914..225620224-chr1:225632867..225635155,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1056607	0.82[CHD][hapmap]
rs10799312	0.91[CHB][hapmap]
rs10915828	0.83[ASW][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs11588279	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12032961	0.83[CHB][hapmap]
rs12034829	0.83[CHB][hapmap]
rs1340865	0.92[CHB][hapmap]
rs1340867	0.88[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891000	0.83[CHB][hapmap]
rs2185529	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766930	0.92[CHB][hapmap]
rs3893032	0.83[CHB][hapmap]
rs499782	0.91[CHB][hapmap]
rs6426075	0.92[CHB][hapmap]
rs6684787	0.89[ASN][1000 genomes]
rs6687980	0.90[ASN][1000 genomes]
rs6696038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697783	0.83[ASW][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs7541888	0.90[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2066233	PYCR2	cis	cerebellum	SCAN
rs2066233	ENAH	cis	normal skin	skin_eQTL
rs2066233	C1orf95	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225616600-225618800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225616600-225618800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:225616600-225622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225616800-225618400	Enhancers	Colon Smooth Muscle	Colon
5	chr1:225617000-225618200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:225617000-225618400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:225617000-225618400	Enhancers	HUVEC	blood vessel
8	chr1:225617200-225618200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:225617200-225618200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:225617200-225618200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:225617200-225618200	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:225617200-225618400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:225617200-225618400	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:225617200-225619000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:225617200-225621200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:225617200-225621200	Weak transcription	Thymus	Thymus
17	chr1:225617400-225618400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr1:225617400-225626600	Weak transcription	Dnd41	blood
19	chr1:225617600-225618400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr1:225618000-225618200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:225618000-225618200	Bivalent Enhancer	NH-A	brain
22	chr1:225618000-225618400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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