Variant report

Variant	rs2475228
Chromosome Location	chr10:116252865-116252866
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	chr10:116245877..116247978-chr10:116251219..116253992,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099204	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11196754	0.80[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1535386	0.82[GIH][hapmap]
rs1923285	0.93[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2145896	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2475226	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2475230	0.91[CHD][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2475231	0.93[ASN][1000 genomes]
rs2497701	0.80[ASN][1000 genomes]
rs2497702	0.98[AFR][1000 genomes]
rs2497703	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6585284	0.85[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs7067793	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7096193	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9421177	0.83[JPT][hapmap];0.80[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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2475228	EMX2	cis	cerebellum	SCAN
rs2475228	AP1M2	trans	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116214600-116263600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:116222200-116264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr10:116225000-116267200	Weak transcription	Aorta	Aorta
4	chr10:116225600-116278800	Weak transcription	HSMM	muscle
5	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
6	chr10:116245000-116258800	Weak transcription	Colonic Mucosa	Colon
7	chr10:116247000-116255200	Weak transcription	Fetal Kidney	kidney
8	chr10:116248000-116258200	Weak transcription	Fetal Intestine Large	intestine
9	chr10:116249600-116264800	Weak transcription	Pancreas	Pancrea
10	chr10:116249800-116259400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:116250000-116256600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:116250000-116256600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:116250000-116256600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:116250000-116258400	Weak transcription	Fetal Intestine Small	intestine
15	chr10:116250000-116259400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:116250200-116256600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:116250200-116256600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr10:116250200-116264600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:116250200-116265200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:116250800-116253000	Enhancers	Ovary	ovary
21	chr10:116251000-116253000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:116251000-116253200	Enhancers	Fetal Lung	lung
23	chr10:116251000-116253200	Enhancers	Fetal Muscle Leg	muscle
24	chr10:116251000-116253200	Enhancers	Stomach Mucosa	stomach
25	chr10:116251000-116259000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr10:116251200-116253000	Enhancers	HMEC	breast
27	chr10:116251400-116253000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr10:116251400-116253200	Enhancers	Thymus	Thymus
29	chr10:116251400-116253600	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr10:116251400-116254600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr10:116251400-116258400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:116251400-116259200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:116251600-116253000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:116251600-116253000	Enhancers	Adipose Nuclei	Adipose
35	chr10:116251600-116253000	Enhancers	Fetal Heart	heart
36	chr10:116251600-116253000	Enhancers	Right Ventricle	heart
37	chr10:116251600-116253000	Enhancers	Small Intestine	intestine
38	chr10:116251600-116253200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr10:116251600-116253200	Enhancers	Primary B cells from peripheral blood	blood
40	chr10:116251600-116253200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:116251600-116253200	Enhancers	GM12878-XiMat	blood
42	chr10:116251600-116254200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr10:116251600-116254200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:116251600-116254600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr10:116251600-116255600	Weak transcription	HSMMtube	muscle
46	chr10:116251800-116253200	Enhancers	H9 Cell Line	embryonic stem cell
47	chr10:116251800-116253200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr10:116251800-116253200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr10:116251800-116253200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr10:116251800-116253200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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