Variant report

Variant	rs4894082
Chromosome Location	chr2:180040659-180040660
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	chr2:180039372..180041323-chr2:180056705..180058266,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10164707	0.82[YRI][hapmap]
rs10164814	0.89[YRI][hapmap]
rs10169713	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181464	0.82[YRI][hapmap]
rs10209887	0.82[YRI][hapmap]
rs10439300	0.82[YRI][hapmap]
rs11687139	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12328184	0.81[EUR][1000 genomes]
rs12617002	0.82[YRI][hapmap]
rs12621115	0.82[YRI][hapmap]
rs12622075	0.82[YRI][hapmap]
rs12693176	0.85[EUR][1000 genomes]
rs12693177	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693178	0.81[JPT][hapmap]
rs12693179	0.82[YRI][hapmap]
rs12987285	0.82[YRI][hapmap]
rs13022632	0.85[EUR][1000 genomes]
rs13382185	0.93[YRI][hapmap]
rs1446673	0.85[EUR][1000 genomes]
rs1844763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1968618	0.95[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs2166534	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4894081	0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs6742744	0.82[TSI][hapmap]
rs6743412	0.93[YRI][hapmap]
rs6759983	0.82[YRI][hapmap]
rs747475	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569887	0.82[YRI][hapmap]
rs7601366	0.93[YRI][hapmap]
rs7608745	0.82[YRI][hapmap]
rs873023	0.82[TSI][hapmap]
rs9653299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4894082	SESTD1	cis	cerebellum	SCAN
rs4894082	EVX2	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
3	chr2:179980000-180056800	Weak transcription	HSMM	muscle
4	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
5	chr2:179996200-180047600	Weak transcription	NH-A	brain
6	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
7	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
8	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
10	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
11	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
13	chr2:180006600-180042000	Weak transcription	Brain Substantia Nigra	brain
14	chr2:180006600-180051000	Weak transcription	HUVEC	blood vessel
15	chr2:180006800-180054600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:180007400-180042200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:180007400-180043000	Weak transcription	Aorta	Aorta
18	chr2:180008400-180042200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:180008600-180048400	Weak transcription	Small Intestine	intestine
20	chr2:180013200-180044400	Weak transcription	Fetal Kidney	kidney
21	chr2:180015000-180041600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:180015000-180043200	Weak transcription	Gastric	stomach
23	chr2:180015000-180054800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:180015000-180060600	Weak transcription	Lung	lung
26	chr2:180015200-180046200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:180015200-180047200	Weak transcription	Placenta	Placenta
28	chr2:180015400-180046000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:180015400-180049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:180015400-180058000	Weak transcription	Fetal Stomach	stomach
31	chr2:180015400-180060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:180015800-180043400	Weak transcription	Liver	Liver
33	chr2:180016000-180049000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:180016000-180054200	Weak transcription	NHDF-Ad	bronchial
35	chr2:180016200-180054000	Weak transcription	Osteobl	bone
36	chr2:180023000-180052800	Weak transcription	Fetal Heart	heart
37	chr2:180024200-180045800	Weak transcription	GM12878-XiMat	blood
38	chr2:180024400-180048600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:180026400-180048800	Weak transcription	Fetal Intestine Small	intestine
40	chr2:180030400-180055400	Weak transcription	Thymus	Thymus
41	chr2:180030800-180046000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:180030800-180050800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:180031200-180052000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:180031400-180042200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:180031400-180050000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:180031800-180042000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:180031800-180042000	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:180031800-180045600	Weak transcription	Fetal Brain Female	brain
49	chr2:180032000-180045000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:180032200-180041800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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