Variant report

Variant	rs862427
Chromosome Location	chr6:38843970-38843971
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	chr6:38843131..38846094-chr6:38848910..38851471,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1018437	1.00[JPT][hapmap]
rs1157884	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1614699	0.89[CEU][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs1678638	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1678640	0.85[ASN][1000 genomes]
rs1678657	0.89[CEU][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs1678669	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1678675	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs1678717	1.00[JPT][hapmap]
rs1678718	1.00[JPT][hapmap]
rs1678725	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1678742	0.80[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1738177	0.80[JPT][hapmap]
rs1738184	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1738192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1738203	1.00[JPT][hapmap]
rs1738220	0.82[JPT][hapmap]
rs1738231	0.87[JPT][hapmap]
rs1738239	1.00[JPT][hapmap]
rs1738240	0.93[JPT][hapmap]
rs1738241	1.00[JPT][hapmap]
rs1738243	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1738247	1.00[JPT][hapmap]
rs1738263	0.93[JPT][hapmap]
rs2395709	1.00[JPT][hapmap]
rs2746170	0.80[JPT][hapmap]
rs34625234	0.82[ASN][1000 genomes]
rs35696175	0.93[ASN][1000 genomes]
rs4286777	1.00[JPT][hapmap]
rs4380739	0.86[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4386804	1.00[JPT][hapmap]
rs4391252	1.00[JPT][hapmap]
rs4443498	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4571559	1.00[JPT][hapmap]
rs4590258	1.00[JPT][hapmap]
rs4711558	0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4711559	0.93[ASN][1000 genomes]
rs4714193	1.00[JPT][hapmap]
rs6458079	0.93[ASN][1000 genomes]
rs6458080	0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6458081	1.00[JPT][hapmap]
rs6931736	1.00[JPT][hapmap]
rs769064	0.80[JPT][hapmap]
rs7746153	0.93[ASN][1000 genomes]
rs7757460	0.86[ASN][1000 genomes]
rs862422	0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs862425	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs862439	1.00[CHB][hapmap]
rs9296265	0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9349100	0.81[ASN][1000 genomes]
rs9357290	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9366982	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9369087	0.83[ASN][1000 genomes]
rs9369089	1.00[JPT][hapmap]
rs9380789	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9380791	0.87[JPT][hapmap]
rs9380795	0.86[ASN][1000 genomes]
rs9380796	1.00[JPT][hapmap]
rs9380798	1.00[JPT][hapmap]
rs9380799	1.00[JPT][hapmap]
rs9394531	0.80[JPT][hapmap]
rs9394544	0.82[ASN][1000 genomes]
rs9394547	1.00[JPT][hapmap]
rs9394550	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs982705	0.84[CHD][hapmap];1.00[JPT][hapmap]

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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs862427	APOBEC2	cis	cerebellum	SCAN
rs862427	KCNK16	cis	cerebellum	SCAN
rs862427	PEX6	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38840200-38845400	Enhancers	Fetal Thymus	thymus
2	chr6:38841000-38844000	Weak transcription	Primary T cells from cord blood	blood
3	chr6:38842200-38844000	Enhancers	Thymus	Thymus
4	chr6:38842200-38845400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:38842200-38845800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:38842800-38844000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr6:38842800-38845400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:38843400-38845400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:38843400-38845600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:38843600-38845000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:38843600-38845400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr6:38843600-38845400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:38843600-38845400	Enhancers	Dnd41	blood
14	chr6:38843800-38844000	Enhancers	Brain Anterior Caudate	brain
15	chr6:38843800-38844200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:38843800-38844400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:38843800-38844600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr6:38843800-38844800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:38843800-38845000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:38843800-38845200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:38843800-38845200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:38843800-38845200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr6:38843800-38845200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:38843800-38845200	Enhancers	Adipose Nuclei	Adipose
25	chr6:38843800-38845400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:38843800-38845400	Enhancers	Primary hematopoietic stem cells	blood
27	chr6:38843800-38845800	Enhancers	Primary monocytes fromperipheralblood	blood

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