Variant report

Variant	rs2920144
Chromosome Location	chr11:4060283-4060284
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	chr11:3862693..3864773-chr11:4060192..4062998,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10742223	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10767807	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10835613	0.85[ASW][hapmap]
rs11030394	0.91[AFR][1000 genomes]
rs11030536	0.85[AFR][1000 genomes]
rs11030841	0.80[MKK][hapmap]
rs11030842	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap]
rs11030853	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11030907	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11030976	0.81[ASW][hapmap];0.81[CHD][hapmap]
rs11604649	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12364664	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419208	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12799265	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12803023	0.93[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs1372804	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.83[MKK][hapmap]
rs1372805	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1662172	0.87[MEX][hapmap]
rs1980412	0.81[CHD][hapmap]
rs2304891	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412344	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2735691	0.81[CHD][hapmap]
rs2920139	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920143	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2923944	0.93[ASW][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2923945	0.95[GIH][hapmap];0.83[AMR][1000 genomes]
rs2923950	0.86[EUR][1000 genomes]
rs2923953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923956	0.85[ASW][hapmap];0.81[MKK][hapmap]
rs2958713	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2958714	0.93[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2959056	0.81[CHB][hapmap];0.95[GIH][hapmap]
rs2959065	0.88[AMR][1000 genomes]
rs2959066	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2959068	0.93[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959070	0.86[CHB][hapmap]
rs2959074	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959075	0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2959079	0.84[AMR][1000 genomes]
rs2959081	0.85[ASW][hapmap];0.81[MKK][hapmap]
rs7102508	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7110060	0.84[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7116520	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7124301	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs747883	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7933164	0.84[MKK][hapmap]
rs7945639	0.84[GIH][hapmap]
rs9704047	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2920144	ART1	cis	parietal	SCAN
rs2920144	OR51A4	cis	parietal	SCAN
rs2920144	RRM1	cis	Artery Tibial	GTEx
rs2920144	TRIM21	cis	cerebellum	SCAN
rs2920144	STIM1	cis	lung	GTEx
rs2920144	CTSD	cis	cerebellum	SCAN
rs2920144	BRSK2	cis	cerebellum	SCAN
rs2920144	OR52I1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
2	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
3	chr11:4046000-4061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:4047400-4061400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:4047800-4077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr11:4048000-4077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr11:4048400-4061400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:4048400-4061800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr11:4048400-4062000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:4048400-4063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:4048400-4065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:4048600-4077800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:4049600-4070600	Weak transcription	Thymus	Thymus
14	chr11:4049800-4065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:4050200-4070800	Weak transcription	Fetal Thymus	thymus
16	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:4051200-4070200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr11:4051400-4065400	Weak transcription	Pancreas	Pancrea
19	chr11:4054800-4065000	Weak transcription	Liver	Liver
20	chr11:4055200-4061800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:4056600-4061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:4057400-4076800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:4058200-4070800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:4058800-4065400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:4058800-4065600	Weak transcription	Primary B cells from cord blood	blood
26	chr11:4058800-4070800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:4059200-4076800	Weak transcription	GM12878-XiMat	blood
28	chr11:4059600-4060400	Strong transcription	Primary T cells from cord blood	blood
29	chr11:4060000-4060400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:4060000-4060400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:4060000-4060400	Enhancers	NHDF-Ad	bronchial
32	chr11:4060000-4060600	Enhancers	Osteobl	bone
33	chr11:4060000-4060800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:4060000-4061400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:4060000-4061400	Weak transcription	HepG2	liver
36	chr11:4060000-4061800	Weak transcription	Psoas Muscle	Psoas
37	chr11:4060200-4060400	Enhancers	Fetal Muscle Leg	muscle
38	chr11:4060200-4060400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:4060200-4061600	Weak transcription	Placenta Amnion	Placenta Amnion

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