Variant report

Variant	rs3813622
Chromosome Location	chr1:161163633-161163634
allele	A/C/G/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161157327..161160707-chr1:161160939..161164830,4	K562	blood:
2	chr1:161122537..161125148-chr1:161162988..161165474,2	K562	blood:
3	chr1:161161386..161164009-chr1:161188467..161191186,2	MCF-7	breast:
4	chr1:161162284..161164231-chr1:161350285..161353157,2	MCF-7	breast:
5	chr1:161162532..161167192-chr1:161195273..161197784,4	K562	blood:
6	chr1:161159866..161163748-chr1:161166740..161171576,6	MCF-7	breast:
7	chr1:161161843..161164361-chr1:161165449..161168112,2	MCF-7	breast:
8	chr1:161163396..161164093-chr1:161352009..161352586,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158859	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000143222	Chromatin interaction
ENSG00000263548	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000268387	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10797094	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265564	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2501876	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4233367	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4564157	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4589131	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656993	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7512012	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv32799	chr1:161161838-161171520	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3813622	FCRL3	cis	parietal	SCAN
rs3813622	DCAF8	cis	cerebellum	SCAN
rs3813622	TAGLN2	cis	parietal	SCAN
rs3813622	B4GALT3	cis	cerebellum	SCAN
rs3813622	OR10J5	cis	cerebellum	SCAN
rs3813622	NES	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161147800-161167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:161148200-161167400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:161148400-161165000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:161153200-161166000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:161153200-161167000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:161156000-161167600	Weak transcription	Fetal Heart	heart
7	chr1:161156200-161166200	Weak transcription	Fetal Lung	lung
8	chr1:161156400-161166000	Weak transcription	Esophagus	oesophagus
9	chr1:161156600-161165200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:161157600-161164400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:161157600-161165000	Weak transcription	Right Atrium	heart
12	chr1:161157600-161167600	Weak transcription	Small Intestine	intestine
13	chr1:161158800-161166000	Weak transcription	Pancreas	Pancrea
14	chr1:161160200-161163800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:161160200-161167000	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:161160200-161167400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:161160400-161164000	Strong transcription	NHLF	lung
18	chr1:161160400-161164400	Genic enhancers	Brain Hippocampus Middle	brain
19	chr1:161160400-161165400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:161160600-161164000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:161160600-161165800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:161160800-161166800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:161161000-161165400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:161161000-161166600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:161161400-161165200	Genic enhancers	Brain Anterior Caudate	brain
26	chr1:161161600-161166000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:161161800-161164600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:161161800-161166000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:161161800-161166200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:161161800-161166400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:161161800-161166400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:161161800-161166600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:161161800-161166600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:161162000-161163800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:161162000-161164800	Enhancers	Brain Angular Gyrus	brain
36	chr1:161162000-161165000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:161162000-161165000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:161162000-161165000	Genic enhancers	Fetal Muscle Leg	muscle
39	chr1:161162000-161165800	Enhancers	Primary T cells from cord blood	blood
40	chr1:161162000-161166800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:161162200-161165000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:161162200-161166400	Enhancers	Primary B cells from cord blood	blood
43	chr1:161162400-161164000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr1:161162400-161164200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr1:161162400-161164600	Enhancers	GM12878-XiMat	blood
46	chr1:161162400-161165400	Enhancers	Fetal Thymus	thymus
47	chr1:161162400-161166600	Genic enhancers	Fetal Stomach	stomach
48	chr1:161162600-161163800	Enhancers	HepG2	liver
49	chr1:161162600-161164000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:161162600-161164000	Enhancers	Placenta	Placenta

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