Variant report

Variant	rs2419111
Chromosome Location	chr10:43300070-43300071
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	chr10:43278278..43279935-chr10:43297692..43300575,2	K562	blood:
2	chr10:43283711..43286231-chr10:43299028..43301664,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RET-4	chr10:43299977-43300625	l_299_chr10:43299976-43307499_brain

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1008751	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10466247	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10751394	0.82[EUR][1000 genomes]
rs10793636	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793638	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10900268	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10900271	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10900273	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10900276	0.83[ASN][1000 genomes]
rs10900278	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11239763	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs11239766	0.83[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs11239774	0.94[ASN][1000 genomes]
rs11239781	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11239782	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11239784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11239785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11239787	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12240444	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12241247	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12570118	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12570505	0.87[LWK][hapmap];0.86[MKK][hapmap]
rs12770094	0.87[ASN][1000 genomes]
rs1539292	0.91[ASN][1000 genomes]
rs1539293	0.99[ASN][1000 genomes]
rs1539294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1575039	0.94[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2142985	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs2419112	0.98[ASN][1000 genomes]
rs34081555	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34109078	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3758514	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs3758516	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3982211	0.83[ASN][1000 genomes]
rs4379783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4948689	0.81[EUR][1000 genomes]
rs4949033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs624804	0.94[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6593491	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6593492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6593494	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs6593495	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs6593496	0.93[ASN][1000 genomes]
rs6593498	0.81[ASN][1000 genomes]
rs6593499	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs7069774	0.95[ASN][1000 genomes]
rs7074877	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs7080924	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7086238	0.89[CHB][hapmap];0.99[ASN][1000 genomes]
rs7089449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7091406	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7133	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7894010	0.81[ASN][1000 genomes]
rs7895230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7896943	0.99[ASN][1000 genomes]
rs7904312	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7909445	0.84[ASN][1000 genomes]
rs7922246	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7922559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9326544	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription 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	35 gene(s)	inside rSNPs	diseases
3	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv895076	chr10:43234432-43326627	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1047838	chr10:43234590-43379219	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription 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 miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv947891	chr10:43299039-43319274	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2419111	MARCH8	cis	parietal	SCAN
rs2419111	BMS1	cis	parietal	SCAN
rs2419111	BMS1	cis	cerebellum	SCAN
rs2419111	HSD17B7P2	cis	cerebellum	SCAN
rs2419111	DHRS12	trans	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43279800-43300200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr10:43279800-43300600	Strong transcription	NH-A	brain
3	chr10:43279800-43302000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:43279800-43302600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:43279800-43303400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:43279800-43303400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:43279800-43303400	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr10:43279800-43303800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr10:43279800-43303800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:43279800-43305000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr10:43279800-43306200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:43279800-43306400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr10:43279800-43307600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr10:43279800-43307800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr10:43279800-43307800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr10:43279800-43308400	Strong transcription	Fetal Intestine Large	intestine
17	chr10:43279800-43308800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:43279800-43309000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr10:43279800-43324000	Strong transcription	Liver	Liver
20	chr10:43279800-43328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:43280000-43300200	Strong transcription	Adipose Nuclei	Adipose
22	chr10:43280000-43301600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:43280000-43301800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:43280000-43301800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:43280000-43303200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:43280000-43303600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr10:43280000-43303600	Strong transcription	HSMM	muscle
28	chr10:43280000-43303600	Strong transcription	Osteobl	bone
29	chr10:43280000-43303800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:43280000-43304600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:43280000-43305000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:43280000-43305800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:43280000-43306400	Strong transcription	Placenta	Placenta
34	chr10:43280000-43306400	Strong transcription	A549	lung
35	chr10:43280000-43306800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:43280000-43309600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr10:43280000-43310800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:43280200-43306000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr10:43280200-43310600	Strong transcription	Primary T cells from cord blood	blood
40	chr10:43280800-43300200	Strong transcription	HUVEC	blood vessel
41	chr10:43281000-43303200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:43281000-43308600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr10:43281800-43306800	Strong transcription	Dnd41	blood
44	chr10:43282400-43308200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr10:43284200-43306400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:43284400-43306400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr10:43285800-43300200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:43285800-43303200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:43286000-43303000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr10:43286200-43302000	Strong transcription	HepG2	liver

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