Variant report

Variant	rs4841401
Chromosome Location	chr8:10489592-10489593
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10483888..10486004-chr8:10489138..10491581,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11778453	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787278	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13259086	0.91[EUR][1000 genomes]
rs7386213	0.84[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7821092	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1031279	chr8:10448142-10501380	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1022682	chr8:10453091-10501380	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
10	nsv539467	chr8:10455842-10495689	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4841401	CLDN23	cis	multi-tissue	Pritchard
rs4841401	C8orf48	cis	cerebellum	SCAN
rs4841401	MFHAS1	cis	cerebellum	SCAN
rs4841401	TDH	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10451800-10490000	Weak transcription	Right Atrium	heart
2	chr8:10485200-10490200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:10485600-10490000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr8:10486000-10492000	Enhancers	Fetal Muscle Leg	muscle
5	chr8:10487400-10489800	Enhancers	Fetal Thymus	thymus
6	chr8:10487400-10490800	Enhancers	Lung	lung
7	chr8:10487400-10491000	Enhancers	Spleen	Spleen
8	chr8:10487600-10490800	Enhancers	Right Ventricle	heart
9	chr8:10487800-10489600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr8:10487800-10490000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr8:10487800-10490000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:10487800-10490200	Enhancers	Primary hematopoietic stem cells	blood
13	chr8:10487800-10490200	Enhancers	HMEC	breast
14	chr8:10488000-10489800	Flanking Active TSS	NH-A	brain
15	chr8:10488000-10490000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:10488000-10490600	Enhancers	Esophagus	oesophagus
17	chr8:10488200-10489800	Enhancers	Brain Anterior Caudate	brain
18	chr8:10488200-10490200	Enhancers	NHEK	skin
19	chr8:10488400-10489600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr8:10488400-10489800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr8:10488400-10489800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr8:10488400-10490000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr8:10488600-10489600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
24	chr8:10488600-10490600	Enhancers	Fetal Muscle Trunk	muscle
25	chr8:10488800-10489600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr8:10489000-10489800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr8:10489000-10489800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr8:10489000-10490000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr8:10489000-10493600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr8:10489000-10494200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:10489200-10489600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:10489200-10489600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:10489200-10489600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr8:10489200-10489600	Active TSS	Adipose Nuclei	Adipose
35	chr8:10489200-10489600	Enhancers	Brain Germinal Matrix	brain
36	chr8:10489200-10489800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:10489400-10489600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr8:10489400-10489600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr8:10489400-10489800	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr8:10489400-10490000	Weak transcription	Placenta	Placenta
41	chr8:10489400-10490200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr8:10489400-10490200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
43	chr8:10489400-10490400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr8:10489400-10490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr8:10489400-10490400	Weak transcription	Left Ventricle	heart
46	chr8:10489400-10490600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr8:10489400-10490600	Enhancers	HUVEC	blood vessel
48	chr8:10489400-10493400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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