Variant report

Variant	rs4820013
Chromosome Location	chr22:30839346-30839347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30685629..30687266-chr22:30839148..30841021,2	K562	blood:
2	chr22:30817233..30818848-chr22:30838471..30840689,2	K562	blood:
3	chr22:30818867..30823842-chr22:30836918..30842867,11	K562	blood:
4	chr22:30765777..30768205-chr22:30839224..30841289,2	K562	blood:
5	chr22:30783511..30785819-chr22:30839208..30841180,2	K562	blood:
6	chr22:30837994..30839939-chr22:30986496..30988737,2	K562	blood:

Variant related genes	Relation type
ENSG00000099999	Chromatin interaction
ENSG00000100029	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000242114	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2412986	0.83[LWK][hapmap]
rs2899150	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs4820854	0.83[LWK][hapmap]
rs5749095	0.85[AFR][1000 genomes]
rs5749104	0.83[LWK][hapmap]
rs5753149	0.97[ASN][1000 genomes]
rs5753161	0.83[LWK][hapmap]
rs5997653	0.83[LWK][hapmap]
rs757663	0.83[LWK][hapmap]
rs9606738	0.87[YRI][hapmap]
rs9608942	0.87[YRI][hapmap]
rs9608944	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv459870	chr22:30836313-30868418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv588886	chr22:30836313-30868418	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4820013	NEFH	cis	parietal	SCAN
rs4820013	RNF215	cis	Heart Left Ventricle	GTEx
rs4820013	SEZ6L	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30831800-30841000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:30832000-30841600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:30832000-30850000	Weak transcription	Right Atrium	heart
4	chr22:30832200-30852400	Weak transcription	Spleen	Spleen
5	chr22:30836400-30840600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr22:30837200-30839600	Enhancers	K562	blood
7	chr22:30837400-30841200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr22:30837600-30839400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr22:30837800-30839400	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr22:30838000-30839400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr22:30838000-30839400	Enhancers	Osteobl	bone
12	chr22:30838000-30839800	Enhancers	Dnd41	blood
13	chr22:30838200-30839400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr22:30838200-30839400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr22:30838200-30839400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr22:30838200-30839400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr22:30838400-30839400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr22:30838400-30839400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr22:30838400-30839400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr22:30838400-30839400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr22:30838400-30839400	Enhancers	Fetal Thymus	thymus
22	chr22:30838400-30839800	Weak transcription	Ovary	ovary
23	chr22:30838400-30841000	Weak transcription	NH-A	brain
24	chr22:30838600-30839400	Enhancers	NHEK	skin
25	chr22:30838800-30839400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr22:30838800-30839400	Enhancers	GM12878-XiMat	blood
27	chr22:30839000-30839400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:30839000-30839400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr22:30839000-30839400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr22:30839000-30839400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr22:30839000-30839400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:30839000-30839400	Enhancers	HMEC	breast
33	chr22:30839000-30839400	Enhancers	HUVEC	blood vessel
34	chr22:30839000-30839400	Enhancers	NHDF-Ad	bronchial
35	chr22:30839000-30841000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr22:30839000-30841000	Enhancers	Hela-S3	cervix
37	chr22:30839200-30839400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr22:30839200-30839400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
39	chr22:30839200-30839400	Enhancers	Left Ventricle	heart
40	chr22:30839200-30839400	Enhancers	HSMM	muscle
41	chr22:30839200-30839400	Enhancers	NHLF	lung
42	chr22:30839200-30839600	Enhancers	Esophagus	oesophagus

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