Variant report

Variant	rs2941591
Chromosome Location	chr2:54908044-54908045
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54907957..54910043-chr2:54910399..54913105,2	MCF-7	breast:
2	chr2:54903042..54905906-chr2:54907957..54909608,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10180713	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10191922	0.90[ASN][1000 genomes]
rs1047499	1.00[ASW][hapmap];0.91[CEU][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs11892788	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12104998	0.86[TSI][hapmap]
rs12105792	1.00[ASW][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs12467581	0.88[EUR][1000 genomes]
rs12468469	0.82[EUR][1000 genomes]
rs12713260	0.82[EUR][1000 genomes]
rs13016942	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs1367295	0.86[TSI][hapmap]
rs1541854	0.86[EUR][1000 genomes]
rs168503	0.86[ASN][1000 genomes]
rs168506	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs171350	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17344072	0.86[TSI][hapmap]
rs17521078	0.86[TSI][hapmap]
rs187124	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs191628	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2292356	0.88[EUR][1000 genomes]
rs2292357	0.84[EUR][1000 genomes]
rs2567835	0.90[ASN][1000 genomes]
rs2931463	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2931464	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2941584	0.82[MEX][hapmap]
rs2941586	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2941587	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2941595	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2971874	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2971875	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2971877	1.00[ASW][hapmap];0.91[CEU][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2971879	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2971883	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2971887	0.88[EUR][1000 genomes]
rs354187	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs354209	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs354213	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs354214	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs354223	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs354224	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs354226	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs354228	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs354231	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs354236	0.83[CHB][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs354237	0.83[CHB][hapmap]
rs354238	0.83[CHB][hapmap]
rs3796014	0.86[EUR][1000 genomes]
rs4444573	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4455199	0.85[EUR][1000 genomes]
rs4519562	0.88[EUR][1000 genomes]
rs4671221	0.83[TSI][hapmap]
rs4671226	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs4671951	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs4671956	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs6545411	0.84[TSI][hapmap]
rs6545415	0.86[TSI][hapmap]
rs6545434	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6706372	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs6729826	0.86[TSI][hapmap]
rs6731661	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6732949	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6734658	0.86[EUR][1000 genomes]
rs6735813	0.84[EUR][1000 genomes]
rs6748816	0.88[EUR][1000 genomes]
rs6761398	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap]
rs7607451	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs907135	0.86[CEU][hapmap];0.83[EUR][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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2941591	SPTBN1	cis	cerebellum	SCAN
rs2941591	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54900000-54908600	Enhancers	NHDF-Ad	bronchial
2	chr2:54901400-54908600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:54903400-54908800	Weak transcription	Spleen	Spleen
4	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
5	chr2:54904800-54908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54905800-54909400	Enhancers	Dnd41	blood
7	chr2:54907000-54908200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:54907000-54908200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:54907000-54908200	Enhancers	Brain Substantia Nigra	brain
10	chr2:54907000-54908600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:54907200-54908200	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:54907200-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:54907400-54908200	Flanking Active TSS	GM12878-XiMat	blood
14	chr2:54907600-54908200	Enhancers	Primary B cells from peripheral blood	blood
15	chr2:54907600-54908200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:54907600-54908200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr2:54907600-54908200	Enhancers	Liver	Liver
18	chr2:54907600-54908200	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:54907600-54908200	Enhancers	Fetal Intestine Large	intestine
20	chr2:54907600-54908200	Enhancers	HMEC	breast
21	chr2:54907600-54908200	Enhancers	HSMMtube	muscle
22	chr2:54907600-54908200	Enhancers	NHEK	skin
23	chr2:54907600-54908200	Enhancers	NHLF	lung
24	chr2:54907600-54908400	Enhancers	HepG2	liver
25	chr2:54907600-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:54907600-54908600	Enhancers	Brain Hippocampus Middle	brain
27	chr2:54907600-54908600	Enhancers	Fetal Thymus	thymus
28	chr2:54907600-54908800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:54907600-54908800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:54907600-54908800	Enhancers	Lung	lung
31	chr2:54907800-54908200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:54907800-54908200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:54907800-54908200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr2:54907800-54908200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:54907800-54908200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:54907800-54908200	Enhancers	Fetal Heart	heart
37	chr2:54907800-54908200	Enhancers	Fetal Muscle Leg	muscle
38	chr2:54907800-54908200	Enhancers	Pancreas	Pancrea
39	chr2:54907800-54908200	Enhancers	NH-A	brain
40	chr2:54907800-54908400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:54907800-54908400	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:54907800-54908600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr2:54907800-54908600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:54907800-54908600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr2:54907800-54908800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr2:54908000-54908200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:54908000-54908200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:54908000-54908200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:54908000-54908200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:54908000-54908200	Enhancers	HSMM	muscle

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