Variant report

Variant	rs544848
Chromosome Location	chr11:85753481-85753482
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85752432..85754152-chr11:85778326..85779927,2	K562	blood:
2	chr11:85753274..85754881-chr11:85905097..85907303,2	MCF-7	breast:
3	chr11:85752345..85755214-chr11:85762057..85763811,2	K562	blood:
4	chr11:85746383..85749282-chr11:85752081..85754619,3	K562	blood:
5	chr11:85752580..85754495-chr11:85817812..85820593,2	K562	blood:
6	chr11:85753212..85755619-chr11:85956266..85958144,2	K562	blood:
7	chr11:85752985..85755269-chr11:85927440..85930207,2	MCF-7	breast:
8	chr11:85752681..85753613-chr11:85986298..85987019,2	K562	blood:
9	chr11:85752848..85754712-chr11:85955507..85958144,2	K562	blood:
10	chr11:85752653..85753611-chr11:85929070..85929776,5	K562	blood:
11	chr11:85752823..85753580-chr11:85929279..85930126,3	MCF-7	breast:
12	chr11:85742480..85744643-chr11:85751587..85754338,2	K562	blood:
13	chr11:85752945..85755603-chr11:85903337..85906078,2	K562	blood:
14	chr11:85752698..85753481-chr11:85904297..85904797,2	MCF-7	breast:
15	chr11:85750753..85754921-chr11:85777860..85781815,4	MCF-7	breast:
16	chr11:85752580..85755769-chr11:85817812..85820593,3	K562	blood:
17	chr11:85579605..85581387-chr11:85752967..85754863,2	MCF-7	breast:
18	chr11:85752937..85753595-chr11:85904443..85905270,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000073921	Chromatin interaction
ENSG00000254699	Chromatin interaction
ENSG00000254502	Chromatin interaction
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1513390	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1996108	0.92[ASN][1000 genomes]
rs2077815	0.84[ASN][1000 genomes]
rs2155051	0.89[ASN][1000 genomes]
rs2458493	0.84[ASN][1000 genomes]
rs2458496	0.83[ASN][1000 genomes]
rs2458500	0.88[ASN][1000 genomes]
rs2508688	0.89[ASN][1000 genomes]
rs2509608	0.88[ASN][1000 genomes]
rs2509609	0.87[ASN][1000 genomes]
rs488134	0.84[ASN][1000 genomes]
rs489486	0.93[ASN][1000 genomes]
rs494369	0.86[ASN][1000 genomes]
rs497711	0.98[ASN][1000 genomes]
rs504129	0.81[ASN][1000 genomes]
rs527162	0.84[ASN][1000 genomes]
rs528109	0.88[ASN][1000 genomes]
rs540422	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs542167	0.89[ASN][1000 genomes]
rs544458	0.92[ASN][1000 genomes]
rs547767	0.89[ASN][1000 genomes]
rs564658	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs583126	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs585820	0.83[ASN][1000 genomes]
rs588076	0.87[ASN][1000 genomes]
rs588380	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs592297	0.86[ASN][1000 genomes]
rs595972	0.83[ASN][1000 genomes]
rs596864	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs597446	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs600258	0.86[ASN][1000 genomes]
rs600743	0.82[ASN][1000 genomes]
rs601185	0.87[ASN][1000 genomes]
rs603615	0.87[ASN][1000 genomes]
rs616555	0.82[ASN][1000 genomes]
rs617836	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618001	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618629	0.87[ASN][1000 genomes]
rs622220	0.91[ASN][1000 genomes]
rs626542	0.82[ASN][1000 genomes]
rs627818	0.88[ASN][1000 genomes]
rs634719	0.95[ASN][1000 genomes]
rs635168	0.92[ASN][1000 genomes]
rs637304	0.82[ASN][1000 genomes]
rs648270	0.87[ASN][1000 genomes]
rs654194	0.83[ASN][1000 genomes]
rs655641	0.90[ASN][1000 genomes]
rs664050	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669556	0.87[ASN][1000 genomes]
rs670606	0.83[ASN][1000 genomes]
rs680119	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs682366	0.84[ASN][1000 genomes]
rs683340	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs683494	0.93[AFR][1000 genomes]
rs7951988	0.84[ASN][1000 genomes]
rs9804630	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	esv1829985	chr11:85740319-85789350	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs544848	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85731600-85754200	Weak transcription	Brain Germinal Matrix	brain
2	chr11:85733200-85754000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:85737200-85755200	Weak transcription	Lung	lung
4	chr11:85737200-85755600	Weak transcription	Esophagus	oesophagus
5	chr11:85740400-85755600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:85740800-85754000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:85742200-85754000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:85742200-85755000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:85742200-85755400	Weak transcription	Aorta	Aorta
10	chr11:85742600-85753800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:85742600-85754000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:85742600-85755600	Weak transcription	Placenta	Placenta
13	chr11:85742800-85758400	Weak transcription	Fetal Intestine Large	intestine
14	chr11:85744800-85753800	Weak transcription	Ovary	ovary
15	chr11:85746600-85753600	Weak transcription	Small Intestine	intestine
16	chr11:85746600-85755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr11:85746600-85762800	Weak transcription	Stomach Mucosa	stomach
18	chr11:85746800-85755600	Weak transcription	Pancreas	Pancrea
19	chr11:85747000-85753800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:85747000-85755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:85748200-85753600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:85749600-85755600	Weak transcription	Fetal Thymus	thymus
23	chr11:85750000-85754000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:85750200-85758200	Weak transcription	Fetal Intestine Small	intestine
25	chr11:85750400-85753800	Weak transcription	Left Ventricle	heart
26	chr11:85750600-85758800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:85751400-85754600	Enhancers	Brain Substantia Nigra	brain
28	chr11:85751400-85761800	Enhancers	Liver	Liver
29	chr11:85751600-85753600	Enhancers	Fetal Heart	heart
30	chr11:85751600-85754200	Enhancers	Brain Angular Gyrus	brain
31	chr11:85751600-85754400	Enhancers	NH-A	brain
32	chr11:85751600-85755400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:85751600-85756400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:85751600-85757600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr11:85751600-85758200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr11:85751800-85754400	Enhancers	Rectal Smooth Muscle	rectum
37	chr11:85751800-85755000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:85751800-85755800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:85751800-85755800	Enhancers	Osteobl	bone
40	chr11:85751800-85756000	Enhancers	HMEC	breast
41	chr11:85751800-85756000	Enhancers	NHLF	lung
42	chr11:85751800-85760600	Enhancers	Primary T cells from cord blood	blood
43	chr11:85751800-85761200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:85752000-85754000	Enhancers	Brain Cingulate Gyrus	brain
45	chr11:85752000-85756000	Enhancers	NHDF-Ad	bronchial
46	chr11:85752200-85753800	Weak transcription	Right Ventricle	heart
47	chr11:85752200-85754400	Enhancers	HUVEC	blood vessel
48	chr11:85752200-85756800	Enhancers	Primary B cells from cord blood	blood
49	chr11:85752400-85754000	Enhancers	HSMMtube	muscle
50	chr11:85752400-85754200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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