Variant report

Variant	rs683340
Chromosome Location	chr11:85658886-85658887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85658069..85660517-chr11:85950815..85953002,2	K562	blood:
2	chr11:85658393..85662131-chr11:85674389..85678033,3	K562	blood:
3	chr11:85658393..85660866-chr11:85673008..85675889,3	K562	blood:
4	chr11:85658382..85661257-chr11:85664114..85666367,2	K562	blood:
5	chr11:85656909..85659832-chr11:85660162..85661872,3	K562	blood:
6	chr11:85657947..85659569-chr11:85955594..85957281,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11234493	0.93[ASN][1000 genomes]
rs1237230	0.91[ASN][1000 genomes]
rs1513390	0.83[EUR][1000 genomes]
rs472618	0.82[ASN][1000 genomes]
rs540422	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs544848	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs556562	0.93[ASN][1000 genomes]
rs564658	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565031	0.84[AFR][1000 genomes]
rs579406	0.93[AFR][1000 genomes]
rs583126	0.83[EUR][1000 genomes]
rs588380	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs596864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597446	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs617836	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs618001	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs626542	0.82[ASN][1000 genomes]
rs664050	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs680119	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs75751	0.98[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	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	nsv1053599	chr11:85641619-85684353	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1040567	chr11:85641619-85684935	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs683340	PICALM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85646600-85660000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:85646600-85667400	Weak transcription	Gastric	stomach
3	chr11:85652800-85664400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:85652800-85668800	Weak transcription	Small Intestine	intestine
5	chr11:85656000-85661000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:85656000-85679800	Weak transcription	Fetal Brain Male	brain
7	chr11:85656200-85661000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:85656400-85660200	Enhancers	Adipose Nuclei	Adipose
9	chr11:85656400-85660200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:85656400-85660200	Enhancers	HUVEC	blood vessel
11	chr11:85656600-85659400	Enhancers	Right Atrium	heart
12	chr11:85656600-85662400	Enhancers	HepG2	liver
13	chr11:85656800-85659000	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr11:85656800-85659600	Enhancers	Brain Cingulate Gyrus	brain
15	chr11:85656800-85660200	Enhancers	Brain Hippocampus Middle	brain
16	chr11:85656800-85661400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:85657000-85659000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:85657000-85659000	Enhancers	Brain Anterior Caudate	brain
19	chr11:85657000-85659400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr11:85657000-85659600	Enhancers	Brain Angular Gyrus	brain
21	chr11:85657000-85660200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr11:85657000-85660600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:85657000-85661000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:85657200-85659400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr11:85657200-85660000	Weak transcription	Placenta	Placenta
26	chr11:85657200-85665600	Weak transcription	Lung	lung
27	chr11:85657400-85659400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr11:85657400-85660400	Enhancers	NHDF-Ad	bronchial
29	chr11:85657400-85660800	Enhancers	Osteobl	bone
30	chr11:85657600-85660400	Enhancers	NHEK	skin
31	chr11:85657600-85665600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:85657600-85666600	Weak transcription	Spleen	Spleen
33	chr11:85657800-85659800	Enhancers	Fetal Lung	lung
34	chr11:85657800-85660400	Enhancers	HMEC	breast
35	chr11:85657800-85661400	Enhancers	GM12878-XiMat	blood
36	chr11:85657800-85664200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr11:85658200-85659200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr11:85658400-85659000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:85658400-85659200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:85658400-85659400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr11:85658400-85659400	Enhancers	Stomach Mucosa	stomach
42	chr11:85658400-85659600	Enhancers	Colon Smooth Muscle	Colon
43	chr11:85658400-85659600	Enhancers	Rectal Smooth Muscle	rectum
44	chr11:85658400-85660200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:85658400-85660200	Enhancers	NHLF	lung
46	chr11:85658400-85660400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:85658400-85666600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:85658400-85667400	Weak transcription	Pancreas	Pancrea
49	chr11:85658600-85659200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:85658600-85659200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links