Variant report

Variant	rs2853085
Chromosome Location	chr11:77123940-77123941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77111729..77114389-chr11:77123441..77126000,2	MCF-7	breast:
2	chr11:77123513..77125266-chr11:77129067..77130720,2	K562	blood:
3	chr11:77120907..77124363-chr11:77182142..77186268,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268635	Chromatin interaction
ENSG00000149269	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1037452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10501425	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10899366	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs10899367	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs10899372	0.87[ASN][1000 genomes]
rs10899373	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10899377	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11237190	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11237198	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11237200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11820118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11828786	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]
rs12223138	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12420360	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12421190	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1453341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17135670	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17135689	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2100393	0.82[AMR][1000 genomes]
rs2154754	0.80[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2156863	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs2282576	0.83[CHD][hapmap];0.80[MEX][hapmap]
rs2467481	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2602460	0.86[ASN][1000 genomes]
rs2602461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2602462	0.89[ASN][1000 genomes]
rs2602471	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2602472	0.93[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2602473	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2602474	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2602475	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2602480	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs2602481	0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs2602482	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2725829	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2725834	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2729749	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2729750	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2729751	0.86[ASN][1000 genomes]
rs2729752	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2729756	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2729757	0.93[ASN][1000 genomes]
rs2729758	0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2729763	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2729772	0.89[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2729775	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2844327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2844335	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2852381	0.87[ASN][1000 genomes]
rs2852383	0.86[ASN][1000 genomes]
rs2852388	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2852389	0.94[ASN][1000 genomes]
rs2852390	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs2853084	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2853089	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2853091	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2853094	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2853095	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2853098	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2888377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3019249	0.81[ASN][1000 genomes]
rs4092275	1.00[ASN][1000 genomes]
rs4944151	0.83[CHD][hapmap];0.80[MEX][hapmap]
rs4944159	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4944160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4945161	0.82[JPT][hapmap]
rs503406	0.82[JPT][hapmap]
rs531638	0.81[ASN][1000 genomes]
rs57305199	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57440754	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs595654	0.81[ASN][1000 genomes]
rs6592721	0.94[ASN][1000 genomes]
rs7105662	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7112264	0.93[ASN][1000 genomes]
rs7120719	0.81[AMR][1000 genomes]
rs724369	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs733358	0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs7944289	0.94[ASN][1000 genomes]
rs876319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs896841	0.89[AMR][1000 genomes]
rs947809	0.99[ASN][1000 genomes]
rs947810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs948959	0.83[CHD][hapmap];0.80[MEX][hapmap]
rs9634030	0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77122200-77124000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:77122800-77124000	Enhancers	Fetal Brain Male	brain
3	chr11:77123000-77124000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:77123000-77124200	Enhancers	Esophagus	oesophagus
5	chr11:77123000-77131400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:77123200-77124000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:77123400-77124000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr11:77123400-77124000	Enhancers	Primary B cells from peripheral blood	blood
9	chr11:77123400-77124000	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr11:77123400-77124000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:77123400-77124000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:77123400-77124000	Enhancers	Brain Anterior Caudate	brain
13	chr11:77123400-77124000	Enhancers	Duodenum Mucosa	Duodenum
14	chr11:77123400-77124000	Enhancers	Fetal Thymus	thymus
15	chr11:77123400-77124000	Enhancers	Stomach Smooth Muscle	stomach
16	chr11:77123400-77124000	Enhancers	GM12878-XiMat	blood
17	chr11:77123400-77124200	Enhancers	Primary T cells from cord blood	blood
18	chr11:77123400-77124200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:77123400-77124200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr11:77123400-77124200	Enhancers	Fetal Intestine Small	intestine
21	chr11:77123400-77124400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:77123400-77124400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr11:77123400-77124400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr11:77123400-77124400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr11:77123400-77124600	Enhancers	Colonic Mucosa	Colon
26	chr11:77123400-77125200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr11:77123400-77125200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:77123400-77131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:77123400-77147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr11:77123400-77147200	Weak transcription	Pancreas	Pancrea
31	chr11:77123600-77124000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr11:77123600-77124000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:77123600-77124000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:77123600-77124000	Enhancers	Brain Germinal Matrix	brain
35	chr11:77123600-77124000	Enhancers	Dnd41	blood
36	chr11:77123600-77124200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:77123600-77124200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr11:77123600-77124200	Enhancers	Fetal Intestine Large	intestine
39	chr11:77123600-77124200	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr11:77123600-77125000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:77123600-77129400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:77123600-77132600	Weak transcription	Stomach Mucosa	stomach
43	chr11:77123600-77135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:77123600-77135800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:77123800-77124200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr11:77123800-77124400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr11:77123800-77124400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:77123800-77124600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr11:77123800-77125400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr11:77123800-77126200	Weak transcription	Fetal Stomach	stomach

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