Variant report

Variant	rs2399046
Chromosome Location	chr3:105189978-105189979
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	chr3:105186048..105188294-chr3:105188492..105191411,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12496827	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13065937	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070223	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13070790	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13075944	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13077096	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13079517	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13079993	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085657	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13092913	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095691	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1438549	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438551	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16851097	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16851175	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34198525	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35616213	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4894926	0.94[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4894928	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66713063	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7431148	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2399046	CBLB	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105179000-105191400	Weak transcription	HSMM	muscle
2	chr3:105179000-105192200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:105179600-105192400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105185200-105191000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105185200-105193000	Weak transcription	Aorta	Aorta
6	chr3:105185800-105192400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:105186000-105190000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:105186200-105192200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:105186200-105194000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:105186400-105190600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:105186400-105190800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:105186400-105191400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:105186400-105191400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:105186400-105192200	Weak transcription	A549	lung
15	chr3:105189000-105190000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:105189000-105190800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:105189200-105190200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:105189400-105190200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:105189600-105190000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:105189600-105190400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:105189600-105190400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:105189600-105190400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr3:105189600-105190400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:105189600-105191000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:105189600-105191600	Enhancers	HUVEC	blood vessel
26	chr3:105189800-105190000	Enhancers	NH-A	brain
27	chr3:105189800-105190000	Enhancers	Osteobl	bone
28	chr3:105189800-105190200	Enhancers	Brain Hippocampus Middle	brain
29	chr3:105189800-105192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:105189800-105192600	Enhancers	Brain Substantia Nigra	brain
31	chr3:105189800-105192800	Enhancers	Brain Inferior Temporal Lobe	brain

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