Variant report

Variant	rs2842462
Chromosome Location	chr6:76010158-76010159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76008575..76011168-chr6:76015563..76017082,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1018471	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10806035	0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10943241	0.81[CHB][hapmap]
rs171263	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2250989	1.00[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240374	0.83[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs240375	0.80[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs240378	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240379	0.84[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240380	0.84[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2748252	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808201	0.83[TSI][hapmap]
rs2808203	0.82[CHB][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2842445	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842446	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842458	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842459	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4275021	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4295446	0.83[ASN][1000 genomes]
rs4374801	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs4541712	0.82[CHB][hapmap]
rs4568415	0.82[CHB][hapmap]
rs4708179	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4708181	0.82[CHB][hapmap]
rs6903526	0.82[CHB][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6904580	0.82[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs6913979	0.82[CHB][hapmap]
rs6929270	0.80[CEU][hapmap];0.82[CHB][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7451911	0.82[CHB][hapmap]
rs7743227	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7766441	0.82[CHB][hapmap]
rs7771904	0.82[CHB][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7772989	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9341514	0.82[CHB][hapmap]
rs9352202	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9359122	0.82[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9443171	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2842462	TMEM30A	cis	cerebellum	SCAN
rs2842462	HMGB1P39	cis	Nerve Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75995200-76016800	Weak transcription	Left Ventricle	heart
2	chr6:75995400-76021800	Weak transcription	Right Ventricle	heart
3	chr6:75995400-76027600	Weak transcription	Aorta	Aorta
4	chr6:75995800-76018200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:75995800-76027200	Weak transcription	Fetal Stomach	stomach
6	chr6:75996000-76022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:76001400-76011800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:76009000-76012200	Enhancers	Colon Smooth Muscle	Colon
9	chr6:76009200-76010200	Enhancers	Stomach Smooth Muscle	stomach
10	chr6:76009200-76010600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:76009200-76012400	Enhancers	Fetal Lung	lung
12	chr6:76009400-76010600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:76009600-76010200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr6:76009600-76010200	Enhancers	H9 Cell Line	embryonic stem cell
15	chr6:76009600-76010200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:76009600-76010200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:76009600-76010200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:76009600-76010200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:76009600-76010200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:76009600-76010200	Enhancers	Liver	Liver
21	chr6:76009600-76010200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:76009600-76010200	Enhancers	Fetal Muscle Leg	muscle
23	chr6:76009600-76010200	Enhancers	Right Atrium	heart
24	chr6:76009600-76010400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:76009600-76010400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:76009600-76010400	Enhancers	Rectal Smooth Muscle	rectum
27	chr6:76009600-76010600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr6:76009600-76010600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:76009600-76010600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:76009600-76011600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:76009800-76010200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:76009800-76010200	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:76009800-76010200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:76009800-76010200	Enhancers	Fetal Heart	heart
35	chr6:76009800-76010200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:76009800-76010200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:76009800-76010200	Enhancers	Small Intestine	intestine
38	chr6:76009800-76010400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr6:76009800-76010400	Enhancers	HUVEC	blood vessel
40	chr6:76009800-76010600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:76009800-76010600	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr6:76009800-76011000	Enhancers	Adipose Nuclei	Adipose
43	chr6:76010000-76010200	Enhancers	Placenta	Placenta
44	chr6:76010000-76010200	Enhancers	Lung	lung
45	chr6:76010000-76010200	Enhancers	Psoas Muscle	Psoas
46	chr6:76010000-76010600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:76010000-76010600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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