Variant report

Variant	rs541829
Chromosome Location	chr11:64997737-64997738
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	chr11:64996294..64998325-chr11:65001503..65003703,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10750761	0.96[ASN][1000 genomes]
rs1195733	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1633466	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1783486	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs1858783	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1877450	0.96[ASN][1000 genomes]
rs239257	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239261	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];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2904966	0.88[CEU][hapmap];0.80[YRI][hapmap]
rs2904967	1.00[JPT][hapmap]
rs2904979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2904980	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2904981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2904982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2904983	0.98[ASN][1000 genomes]
rs2904984	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2904986	0.80[ASN][1000 genomes]
rs2957111	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3015997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015999	0.85[ASN][1000 genomes]
rs3016001	0.93[ASN][1000 genomes]
rs3016002	0.92[ASN][1000 genomes]
rs482842	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs487989	1.00[JPT][hapmap]
rs499027	0.80[ASN][1000 genomes]
rs503277	1.00[JPT][hapmap]
rs506280	1.00[JPT][hapmap]
rs507005	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs526502	0.80[ASN][1000 genomes]
rs554122	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs560097	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs571128	0.85[ASN][1000 genomes]
rs592050	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs611910	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs612392	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs620427	0.88[CEU][hapmap]
rs625427	0.98[ASN][1000 genomes]
rs626555	1.00[JPT][hapmap]
rs626802	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs630055	1.00[JPT][hapmap]
rs655433	1.00[JPT][hapmap]
rs6591180	0.85[YRI][hapmap]
rs667341	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs668735	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs673147	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs676114	0.86[YRI][hapmap]
rs676573	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs689288	0.88[CEU][hapmap]
rs7111907	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7116674	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs8638	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64977400-64998400	Weak transcription	Small Intestine	intestine
2	chr11:64993400-65000000	Weak transcription	A549	lung
3	chr11:64993600-64999400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:64993600-64999400	Weak transcription	NHLF	lung
5	chr11:64993600-64999800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:64993600-65001400	Weak transcription	Right Ventricle	heart
7	chr11:64993600-65011000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:64993800-64998400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:64993800-64998400	Weak transcription	Brain Substantia Nigra	brain
10	chr11:64993800-64998600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:64993800-64999600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:64993800-65003800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:64993800-65004000	Weak transcription	Esophagus	oesophagus
14	chr11:64993800-65010800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:64993800-65010800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:64994000-64998200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:64994000-64998400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:64994000-64999400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:64994000-64999600	Weak transcription	Liver	Liver
20	chr11:64994000-65000400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:64994000-65003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:64994200-64997800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:64994200-64998600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:64994200-64999400	Weak transcription	HMEC	breast
25	chr11:64994200-65003800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:64994200-65007200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:64996400-64999800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:64996800-64997800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:64996800-64997800	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr11:64996800-64998000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:64997000-64997800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:64997000-65000200	Weak transcription	Lung	lung
33	chr11:64997200-65001800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:64997600-64998000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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