Variant report

Variant	rs4397861
Chromosome Location	chr11:66647188-66647189
allele	C/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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66620817..66623976-chr11:66646170..66651314,5	MCF-7	breast:
2	chr11:66646263..66648059-chr11:66724688..66727325,2	MCF-7	breast:
3	chr11:66632881..66640228-chr11:66642679..66650860,16	MCF-7	breast:
4	chr11:66633380..66638665-chr11:66646589..66650033,7	MCF-7	breast:
5	chr11:66642783..66644692-chr11:66646409..66648155,2	MCF-7	breast:
6	chr11:66645757..66648889-chr11:66656797..66659524,3	MCF-7	breast:
7	chr11:66644476..66647274-chr11:66681584..66683637,2	MCF-7	breast:
8	chr11:66646725..66648857-chr11:66724586..66727016,2	MCF-7	breast:
9	chr11:66647175..66649166-chr11:66649230..66650803,2	MCF-7	breast:
10	chr11:66647154..66650016-chr11:66659832..66661470,2	MCF-7	breast:
11	chr11:66608285..66612923-chr11:66645683..66650712,11	MCF-7	breast:
12	chr11:66622201..66627158-chr11:66645726..66651981,9	MCF-7	breast:
13	chr11:66624012..66626938-chr11:66646226..66647992,2	MCF-7	breast:
14	chr11:66646522..66648593-chr11:66737895..66740252,2	K562	blood:
15	chr11:66645590..66647699-chr11:66725048..66727019,2	K562	blood:
16	chr11:66647060..66650897-chr11:66788816..66791425,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173621	Chromatin interaction
ENSG00000173227	Chromatin interaction
ENSG00000173653	Chromatin interaction
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1127145	1.00[ASN][1000 genomes]
rs11828542	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17147932	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs17498954	1.00[CHB][hapmap]
rs2380757	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2380758	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802743	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867133	1.00[CHB][hapmap]
rs4500496	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[ASN][1000 genomes]
rs56803995	1.00[ASN][1000 genomes]
rs57240313	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57410747	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57466874	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58800112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59538303	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59550560	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59932755	1.00[ASN][1000 genomes]
rs60651024	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61634527	1.00[ASN][1000 genomes]
rs735498	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs7952232	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4397861	CELSR3	trans	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66625000-66648800	Weak transcription	Right Atrium	heart
2	chr11:66625400-66648000	Weak transcription	Left Ventricle	heart
3	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:66625800-66650800	Weak transcription	Osteobl	bone
5	chr11:66627800-66650000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:66633600-66648000	Weak transcription	Psoas Muscle	Psoas
7	chr11:66636600-66648000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:66636800-66647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:66636800-66647800	Weak transcription	Thymus	Thymus
10	chr11:66636800-66648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:66636800-66650800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:66638000-66650000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:66638600-66650200	Weak transcription	Fetal Intestine Large	intestine
14	chr11:66639000-66648000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:66639000-66657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:66639200-66647800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:66639200-66649600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:66639200-66649800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:66639200-66657400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:66639400-66648000	Weak transcription	Lung	lung
21	chr11:66639400-66648200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:66639400-66650000	Weak transcription	Colonic Mucosa	Colon
23	chr11:66639400-66650400	Weak transcription	Aorta	Aorta
24	chr11:66639400-66659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:66639600-66650200	Weak transcription	Fetal Intestine Small	intestine
26	chr11:66639800-66647600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:66643000-66647400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:66643000-66647800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:66643200-66651400	Enhancers	Fetal Muscle Leg	muscle
30	chr11:66643200-66653000	Enhancers	Liver	Liver
31	chr11:66643800-66648600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:66643800-66649800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:66644200-66648800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:66644400-66647400	Weak transcription	K562	blood
35	chr11:66644600-66647800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr11:66644600-66650800	Weak transcription	HepG2	liver
37	chr11:66645200-66647200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:66645200-66647600	Enhancers	Hela-S3	cervix
39	chr11:66645200-66648600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:66645200-66652000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:66645400-66647200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr11:66645400-66648400	Enhancers	Fetal Stomach	stomach
43	chr11:66645400-66648600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:66645400-66651200	Enhancers	Gastric	stomach
45	chr11:66645400-66651200	Enhancers	HMEC	breast
46	chr11:66645600-66648000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:66645600-66648600	Enhancers	Placenta	Placenta
48	chr11:66645600-66650000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:66645600-66650800	Enhancers	Fetal Thymus	thymus
50	chr11:66645600-66652400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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