Variant report

Variant	rs527162
Chromosome Location	chr11:85715736-85715737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85714087-85719397	K562	blood:	n/a	n/a
2	STAT3	chr11:85715630-85715784	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85708264..85711014-chr11:85715226..85717341,2	MCF-7	breast:

Variant related genes	Relation type
PICALM	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10751134	0.87[ASW][hapmap];0.89[LWK][hapmap];0.82[YRI][hapmap]
rs10792832	0.82[YRI][hapmap]
rs11234493	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1237230	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1996108	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2077815	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2155051	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2458493	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2458496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2458499	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458500	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2508688	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2508696	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs2509608	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2509609	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3016327	0.82[AMR][1000 genomes]
rs3851179	0.87[ASW][hapmap]
rs472618	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs493254	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs494369	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944549	0.81[AMR][1000 genomes]
rs497711	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs504129	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs528109	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536841	0.86[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs540422	0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs542167	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs544458	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs544848	0.84[ASN][1000 genomes]
rs547767	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs548121	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556562	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs564658	0.92[ASN][1000 genomes]
rs585820	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs588076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs588380	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs592297	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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592314	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs595972	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597446	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs600258	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602222	0.86[CHB][hapmap]
rs602391	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs603615	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs616555	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs617836	0.90[ASN][1000 genomes]
rs618001	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs618629	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs618679	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626542	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs627818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs635168	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs636355	0.83[AFR][1000 genomes]
rs637304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645299	0.89[CHB][hapmap]
rs648270	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654194	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655641	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs659801	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664050	0.94[ASN][1000 genomes]
rs669556	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs669813	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs670606	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs676733	0.87[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap]
rs677909	1.00[ASW][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs680119	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs682366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682928	0.85[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs694011	0.82[YRI][hapmap]
rs75751	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7938033	0.86[CHB][hapmap];0.80[CHD][hapmap];0.80[ASN][1000 genomes]
rs7941541	1.00[ASW][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap]
rs7951988	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804630	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1048818	chr11:85524635-85746473	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv541116	chr11:85524635-85746473	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1053808	chr11:85588919-85757693	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
7	nsv468769	chr11:85683554-85757589	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv555641	chr11:85683554-85757589	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv898054	chr11:85683554-85772636	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv469975	chr11:85688209-85729372	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv468770	chr11:85688209-85751883	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv555642	chr11:85688209-85751883	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv468771	chr11:85688209-85757589	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv468773	chr11:85688209-85757589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv555643	chr11:85688209-85757589	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv468774	chr11:85688209-85775059	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv555644	chr11:85688209-85775059	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs527162	ME3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85659400-85745800	Weak transcription	Stomach Mucosa	stomach
2	chr11:85663800-85740200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:85664400-85726800	Strong transcription	Liver	Liver
4	chr11:85664400-85729000	Strong transcription	Placenta	Placenta
5	chr11:85664600-85730800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:85664800-85733000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:85665200-85742600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:85665200-85743000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:85666000-85735800	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr11:85670000-85715800	Weak transcription	Colonic Mucosa	Colon
11	chr11:85675000-85742600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr11:85680600-85731600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:85680800-85725600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:85681000-85725800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:85681000-85729400	Strong transcription	NH-A	brain
16	chr11:85695200-85725200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:85695200-85725200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:85696200-85722800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr11:85696600-85729000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:85697000-85719400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:85697400-85733400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr11:85697600-85719400	Strong transcription	HSMM	muscle
23	chr11:85697800-85726400	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:85697800-85742600	Strong transcription	HUVEC	blood vessel
25	chr11:85698800-85718000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:85699600-85719600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr11:85699600-85727400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr11:85700400-85729400	Strong transcription	Osteobl	bone
29	chr11:85700600-85731600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:85700600-85742400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:85701000-85745000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:85702000-85732000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr11:85702000-85732000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:85702600-85725600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:85702600-85727800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:85702800-85722400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:85702800-85722600	Strong transcription	GM12878-XiMat	blood
38	chr11:85702800-85729200	Strong transcription	Fetal Thymus	thymus
39	chr11:85703000-85723000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:85703200-85742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:85703400-85724200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:85703600-85719400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:85703600-85719800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:85703800-85719800	Strong transcription	Dnd41	blood
45	chr11:85704000-85715800	Strong transcription	HepG2	liver
46	chr11:85704000-85719000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr11:85704200-85719800	Strong transcription	Primary B cells from cord blood	blood
48	chr11:85707200-85718200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:85707200-85719600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:85707800-85717600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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