Variant report

Variant	rs1483138
Chromosome Location	chr2:142292473-142292474
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	chr2:142291504..142294290-chr2:142295014..142296558,2	MCF-7	breast:
2	chr2:142288498..142290059-chr2:142292199..142295076,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10165850	0.83[AFR][1000 genomes]
rs10165979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10167487	0.85[YRI][hapmap]
rs10170114	0.83[AFR][1000 genomes]
rs10176397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187180	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10191434	0.83[YRI][hapmap]
rs10200529	0.81[YRI][hapmap];0.94[AFR][1000 genomes]
rs10200578	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200582	0.85[AFR][1000 genomes]
rs10200782	1.00[AMR][1000 genomes]
rs10200845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1038346	0.85[YRI][hapmap]
rs11887261	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904458	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12466189	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12472734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12617980	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12618575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691613	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691614	1.00[AMR][1000 genomes]
rs12691615	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483152	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1905292	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2128694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2170667	1.00[AMR][1000 genomes]
rs2200190	1.00[YRI][hapmap]
rs2220071	1.00[YRI][hapmap]
rs2381110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381111	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381192	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3856360	0.85[YRI][hapmap]
rs3935992	1.00[AMR][1000 genomes]
rs4008531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4245859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4264515	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4296372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4359580	0.85[YRI][hapmap];0.96[AFR][1000 genomes]
rs4366842	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4396652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4439901	1.00[AMR][1000 genomes]
rs4441406	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4476294	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4477847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4482418	0.85[YRI][hapmap];0.94[AFR][1000 genomes]
rs4482419	0.92[AFR][1000 genomes]
rs4536595	1.00[YRI][hapmap]
rs4538137	1.00[YRI][hapmap]
rs4555282	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4954909	1.00[AMR][1000 genomes]
rs4954913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429897	0.84[AFR][1000 genomes]
rs6429901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429902	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706356	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706377	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707422	0.85[YRI][hapmap]
rs6707441	0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6708438	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710020	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6713043	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718844	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6744340	1.00[YRI][hapmap]
rs6749472	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7557631	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7571511	0.84[AFR][1000 genomes]
rs7572480	1.00[AMR][1000 genomes]
rs7582623	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7585325	1.00[AMR][1000 genomes]
rs7590820	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs7593866	1.00[AMR][1000 genomes]
rs7607376	1.00[AMR][1000 genomes]
rs900472	0.91[YRI][hapmap]
rs983197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983198	0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs988330	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv459640	chr2:142291211-142345574	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv583213	chr2:142291211-142345574	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142291200-142293200	Enhancers	Primary hematopoietic stem cells	blood
2	chr2:142291200-142293400	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:142291200-142293400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:142291600-142293200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:142291600-142293400	Enhancers	Primary T cells from cord blood	blood
6	chr2:142291600-142293400	Enhancers	Brain Hippocampus Middle	brain
7	chr2:142291800-142293000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:142291800-142293400	Enhancers	Dnd41	blood
9	chr2:142292000-142292800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:142292000-142292800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:142292000-142293000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:142292000-142293000	Flanking Active TSS	GM12878-XiMat	blood
13	chr2:142292000-142293400	Enhancers	Brain Angular Gyrus	brain
14	chr2:142292200-142292600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:142292200-142292600	Active TSS	Brain Anterior Caudate	brain
16	chr2:142292200-142292600	Active TSS	Stomach Smooth Muscle	stomach
17	chr2:142292200-142292800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:142292200-142292800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:142292200-142292800	Enhancers	Fetal Brain Female	brain
20	chr2:142292200-142292800	Enhancers	Fetal Heart	heart
21	chr2:142292200-142292800	Enhancers	Fetal Stomach	stomach
22	chr2:142292200-142293000	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:142292400-142292600	Enhancers	Primary B cells from cord blood	blood
24	chr2:142292400-142292600	Active TSS	Brain Substantia Nigra	brain
25	chr2:142292400-142292800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:142292400-142292800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:142292400-142292800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:142292400-142292800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:142292400-142292800	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr2:142292400-142293000	Enhancers	Colon Smooth Muscle	Colon

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