Variant report

Variant	rs2854712
Chromosome Location	chr2:209000738-209000739
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:208995156..208996689-chr2:208999145..209001053,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1008487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124651	0.85[ASN][1000 genomes]
rs12328374	0.92[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs12472511	0.85[ASN][1000 genomes]
rs1470826	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2289917	0.81[MEX][hapmap]
rs2362791	0.85[ASN][1000 genomes]
rs2362792	0.85[ASN][1000 genomes]
rs2601478	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2601479	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2601481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854711	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2854723	0.85[ASN][1000 genomes]
rs2885602	0.85[ASN][1000 genomes]
rs34472829	0.89[EUR][1000 genomes]
rs4485502	0.85[ASN][1000 genomes]
rs57005437	0.85[ASN][1000 genomes]
rs62192856	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62194791	0.81[ASN][1000 genomes]
rs6732496	0.92[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv875747	chr2:208990345-209042963	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv875748	chr2:208994399-209033557	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2854712	CRYGA	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208993400-209002200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:208994600-209002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:208998800-209002000	Enhancers	Fetal Intestine Small	intestine
4	chr2:208998800-209002400	Enhancers	Fetal Intestine Large	intestine
5	chr2:208999000-209000800	Enhancers	Primary hematopoietic stem cells	blood
6	chr2:208999000-209000800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:208999200-209002200	Enhancers	HepG2	liver
8	chr2:208999400-209000800	Enhancers	Fetal Thymus	thymus
9	chr2:208999400-209000800	Enhancers	Dnd41	blood
10	chr2:208999600-209000800	Enhancers	Primary T cells from cord blood	blood
11	chr2:208999600-209002000	Enhancers	Ovary	ovary
12	chr2:208999600-209002000	Enhancers	Stomach Mucosa	stomach
13	chr2:208999800-209000800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:209000000-209000800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:209000000-209000800	Enhancers	Small Intestine	intestine
16	chr2:209000200-209001000	Enhancers	Liver	Liver
17	chr2:209000200-209001600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:209000400-209000800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:209000400-209000800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr2:209000400-209000800	Enhancers	Right Atrium	heart
21	chr2:209000400-209001400	Weak transcription	HMEC	breast
22	chr2:209000400-209001800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr2:209000600-209000800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:209000600-209001600	Weak transcription	Placenta	Placenta
25	chr2:209000600-209001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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