Variant report

Variant	rs10488818
Chromosome Location	chr11:35312380-35312381
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	chr11:35310052..35313543-chr11:35317974..35319677,3	MCF-7	breast:
2	chr11:35295688..35300934-chr11:35309144..35319083,18	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1042113	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444271	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10488816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10488817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10836368	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033050	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033056	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11033057	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033060	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033063	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033064	1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11033071	0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs11033080	0.85[JPT][hapmap]
rs12146523	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418812	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574069	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12576364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12576375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16927292	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2236272	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794087	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3794088	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794094	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794097	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829266	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3847612	0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs3847613	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs3847620	0.85[JPT][hapmap]
rs3891872	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3895234	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3911898	0.89[JPT][hapmap]
rs4083481	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs41352148	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41427147	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs41525047	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756207	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4756211	0.84[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap]
rs4756219	0.85[JPT][hapmap]
rs4756220	0.85[JPT][hapmap]
rs4756221	0.85[JPT][hapmap]
rs56043665	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56140126	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56402269	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61880962	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61882290	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61882291	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61882292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61882293	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102949	0.96[YRI][hapmap]
rs7111043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111055	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111179	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7115246	0.81[YRI][hapmap]
rs7129693	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638196	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638197	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs752949	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7927975	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7934047	0.85[JPT][hapmap]
rs7940391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10488818	C11orf41	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35298000-35317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:35298200-35326000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:35299000-35326600	Weak transcription	Brain Hippocampus Middle	brain
4	chr11:35299800-35328600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:35302400-35327000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:35302600-35329000	Weak transcription	Brain Angular Gyrus	brain
7	chr11:35304000-35324800	Weak transcription	Liver	Liver
8	chr11:35304600-35314200	Weak transcription	Stomach Mucosa	stomach
9	chr11:35304600-35317000	Weak transcription	Pancreas	Pancrea
10	chr11:35304600-35326600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:35308000-35324000	Weak transcription	HepG2	liver
12	chr11:35308400-35313600	Weak transcription	Fetal Brain Male	brain
13	chr11:35308600-35325800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:35308600-35326400	Weak transcription	Brain Anterior Caudate	brain
15	chr11:35308800-35313000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:35309000-35312800	Enhancers	NHDF-Ad	bronchial
17	chr11:35309400-35312600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:35309400-35312600	Enhancers	HSMMtube	muscle
19	chr11:35309600-35312600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:35309600-35312600	Enhancers	HSMM	muscle
21	chr11:35309600-35312800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr11:35309800-35312600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:35309800-35312600	Enhancers	NHLF	lung
24	chr11:35309800-35318400	Weak transcription	Fetal Brain Female	brain
25	chr11:35310000-35312600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:35310000-35312800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:35310000-35325800	Weak transcription	Brain Germinal Matrix	brain
28	chr11:35310200-35313000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:35310200-35313600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:35310600-35312600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:35310600-35312600	Enhancers	NHEK	skin
32	chr11:35310600-35312800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:35310800-35313800	Weak transcription	GM12878-XiMat	blood
34	chr11:35311000-35314400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:35311800-35312600	Enhancers	NH-A	brain
36	chr11:35311800-35314600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:35311800-35315200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:35312000-35312400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:35312000-35317200	Weak transcription	HMEC	breast
40	chr11:35312000-35324000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:35312200-35313400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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