Variant report

Variant	rs11828786
Chromosome Location	chr11:77169828-77169829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77168519..77171597-chr11:77180665..77182753,3	MCF-7	breast:
2	chr11:77168629..77170251-chr11:77183087..77185478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268635	Chromatin interaction
ENSG00000149269	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1037452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10501425	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10899372	0.82[ASN][1000 genomes]
rs10899373	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10899377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11237190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11237198	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11237200	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11820118	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12223138	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12420360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12421190	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1453341	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17135670	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135689	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2100393	0.82[AMR][1000 genomes]
rs2154754	0.94[JPT][hapmap]
rs2156863	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2467481	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2602460	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602462	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2602472	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs2602473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2602474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2602475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2602480	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2602481	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs2602482	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2725829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2725834	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729749	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729750	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729751	0.93[ASN][1000 genomes]
rs2729752	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2729756	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2729757	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2729758	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2729763	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2729772	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2729775	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844327	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2844335	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2852381	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2852383	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2852389	0.99[ASN][1000 genomes]
rs2852390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2853084	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853085	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2853089	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs2853091	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2853094	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2853095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2888377	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3019249	0.83[AFR][1000 genomes]
rs4092275	0.93[ASN][1000 genomes]
rs4944159	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4944160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs503406	0.83[JPT][hapmap]
rs57305199	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57440754	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6592721	0.99[ASN][1000 genomes]
rs7105662	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7112264	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120719	0.81[AMR][1000 genomes]
rs724369	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs733358	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7944289	0.99[ASN][1000 genomes]
rs876319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs896841	0.89[AMR][1000 genomes]
rs947809	0.94[ASN][1000 genomes]
rs947810	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic 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	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic 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	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:77160600-77178000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:77161000-77170200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:77163000-77173400	Weak transcription	Placenta	Placenta
6	chr11:77165000-77172200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:77165200-77170800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:77165800-77171200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr11:77166200-77172800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr11:77167800-77182000	Weak transcription	Fetal Kidney	kidney
11	chr11:77168000-77170400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:77168200-77170200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:77168400-77170600	Enhancers	Brain Hippocampus Middle	brain
14	chr11:77168400-77172200	Enhancers	Fetal Intestine Small	intestine
15	chr11:77168600-77170000	Weak transcription	Primary B cells from cord blood	blood
16	chr11:77168600-77170400	Enhancers	Stomach Mucosa	stomach
17	chr11:77168600-77173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:77168600-77173600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:77168600-77178800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:77168800-77170000	Weak transcription	Small Intestine	intestine
21	chr11:77168800-77170000	Weak transcription	NH-A	brain
22	chr11:77168800-77170400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr11:77168800-77170600	Weak transcription	Psoas Muscle	Psoas
24	chr11:77168800-77179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:77169000-77170000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr11:77169000-77170000	Weak transcription	Brain Germinal Matrix	brain
27	chr11:77169000-77170200	Weak transcription	Brain Anterior Caudate	brain
28	chr11:77169000-77171000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:77169000-77173000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr11:77169000-77174600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:77169000-77175200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:77169000-77181400	Weak transcription	Brain Angular Gyrus	brain
33	chr11:77169200-77173000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr11:77169400-77170400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr11:77169400-77170600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr11:77169600-77170000	Enhancers	Brain Cingulate Gyrus	brain
37	chr11:77169600-77171000	Weak transcription	Brain Substantia Nigra	brain
38	chr11:77169800-77170000	Enhancers	Liver	Liver
39	chr11:77169800-77170000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr11:77169800-77170000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr11:77169800-77170400	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr11:77169800-77170400	Enhancers	A549	lung
43	chr11:77169800-77170600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr11:77169800-77170600	Enhancers	Fetal Intestine Large	intestine
45	chr11:77169800-77170600	Flanking Active TSS	GM12878-XiMat	blood
46	chr11:77169800-77170800	Enhancers	HepG2	liver

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