Variant report

Variant	rs11015650
Chromosome Location	chr10:27580373-27580374
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	chr10:27528037..27532536-chr10:27578787..27581374,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000262412	Chromatin interaction
ENSG00000107897	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10829222	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829223	0.87[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829224	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10829225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829226	0.80[ASN][1000 genomes]
rs10829227	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829228	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10829229	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10829233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829235	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11015635	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015637	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015640	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11015642	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015643	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015644	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015646	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015655	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11015657	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015691	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12355234	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1832019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1832020	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1832021	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2184165	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718925	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35724729	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35891243	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818746	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4396190	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4607976	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4617487	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61849692	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61849713	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61849720	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7076087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9664367	0.85[AMR][1000 genomes]
rs9665037	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1045257	chr10:27572440-27926946	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv550242	chr10:27577568-27705855	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv550243	chr10:27577773-27705855	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11015650	RP11-748L13.6	cis	Thyroid	GTEx
rs11015650	ARMC4P1	cis	Esophagus Muscularis	GTEx
rs11015650	ARMC4P1	cis	Thyroid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27579600-27580400	Enhancers	Spleen	Spleen
2	chr10:27579800-27580400	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr10:27579800-27580400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr10:27579800-27580800	Enhancers	Primary T cells from cord blood	blood
5	chr10:27580000-27580400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr10:27580000-27580400	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:27580000-27580400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:27580000-27580400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:27580000-27580400	Enhancers	Thymus	Thymus
10	chr10:27580000-27580600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr10:27580000-27580600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr10:27580000-27580600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:27580000-27581000	Flanking Active TSS	Dnd41	blood
14	chr10:27580200-27580400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:27580200-27580400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr10:27580200-27580400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr10:27580200-27580400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:27580200-27580400	Flanking Active TSS	Liver	Liver
19	chr10:27580200-27580400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr10:27580200-27580400	Flanking Active TSS	GM12878-XiMat	blood
21	chr10:27580200-27580400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr10:27580200-27580600	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:27580200-27580600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr10:27580200-27580600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr10:27580200-27580800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr10:27580200-27580800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr10:27580200-27581000	Active TSS	Primary B cells from cord blood	blood
28	chr10:27580200-27581200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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