Variant report

Variant	rs4449112
Chromosome Location	chr2:209000573-209000574
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	chr2:208995156..208996689-chr2:208999145..209001053,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11678616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679743	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471551	0.81[AMR][1000 genomes]
rs13007922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392731	0.88[MEX][hapmap]
rs2242071	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs4263096	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4276012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4289171	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4338947	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375849	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583446	0.94[JPT][hapmap]
rs6435416	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710715	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711499	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751246	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578859	0.88[MEX][hapmap]
rs796287	0.81[ASN][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
rs4449112	C2orf67	cis	parietal	SCAN

Chromatin state (count:28 , 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	chr2:208999200-209000600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:208999200-209000600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:208999200-209002200	Enhancers	HepG2	liver
10	chr2:208999400-209000600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:208999400-209000800	Enhancers	Fetal Thymus	thymus
12	chr2:208999400-209000800	Enhancers	Dnd41	blood
13	chr2:208999600-209000600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:208999600-209000800	Enhancers	Primary T cells from cord blood	blood
15	chr2:208999600-209002000	Enhancers	Ovary	ovary
16	chr2:208999600-209002000	Enhancers	Stomach Mucosa	stomach
17	chr2:208999800-209000600	Enhancers	Placenta	Placenta
18	chr2:208999800-209000600	Enhancers	Pancreas	Pancrea
19	chr2:208999800-209000800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:209000000-209000800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:209000000-209000800	Enhancers	Small Intestine	intestine
22	chr2:209000200-209001000	Enhancers	Liver	Liver
23	chr2:209000200-209001600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:209000400-209000800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:209000400-209000800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr2:209000400-209000800	Enhancers	Right Atrium	heart
27	chr2:209000400-209001400	Weak transcription	HMEC	breast
28	chr2:209000400-209001800	Enhancers	Pancreatic Islets	Pancreatic Islet

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