Variant report

Variant	rs4400599
Chromosome Location	chr1:154127100-154127101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154121866..154123799-chr1:154125577..154127582,4	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10908739	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12063830	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2494663	0.85[CEU][hapmap]
rs2790690	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs3001362	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3001363	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072431	0.81[GIH][hapmap]
rs4364874	0.81[GIH][hapmap]
rs4540651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4579747	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845364	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845605	0.85[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7521047	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs7537213	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4400599	S100A8	cis	parietal	SCAN
rs4400599	SF3B4	cis	parietal	SCAN
rs4400599	DENND4B	cis	parietal	SCAN
rs4400599	SLC27A3	cis	cerebellum	SCAN
rs4400599	FLG	cis	parietal	SCAN
rs4400599	CKS1B	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154123800-154127400	Weak transcription	Adipose Nuclei	Adipose
3	chr1:154124000-154127200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:154124000-154127800	Weak transcription	Small Intestine	intestine
5	chr1:154124000-154128000	Weak transcription	NHDF-Ad	bronchial
6	chr1:154124200-154127600	Weak transcription	Osteobl	bone
7	chr1:154124400-154127200	Weak transcription	Right Atrium	heart
8	chr1:154124400-154127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:154124400-154127400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:154124400-154129800	Weak transcription	Left Ventricle	heart
11	chr1:154125000-154130400	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:154125200-154127600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:154125200-154131000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:154125400-154128000	Weak transcription	Stomach Mucosa	stomach
15	chr1:154125600-154127200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:154125600-154127200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:154125600-154127200	Weak transcription	Fetal Brain Female	brain
18	chr1:154125600-154127200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:154125600-154128000	Weak transcription	NHEK	skin
20	chr1:154125600-154129800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:154125600-154129800	Weak transcription	Gastric	stomach
22	chr1:154125600-154130000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:154125800-154127400	Weak transcription	Liver	Liver
24	chr1:154125800-154127600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:154125800-154127600	Weak transcription	Hela-S3	cervix
26	chr1:154125800-154129600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:154126000-154127200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:154126000-154128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:154126200-154128200	Genic enhancers	Primary T cells from cord blood	blood
30	chr1:154126200-154128600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells	blood
32	chr1:154126200-154128800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:154126200-154129400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:154126200-154129400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:154126200-154129600	Weak transcription	HSMMtube	muscle
36	chr1:154126200-154130400	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr1:154126400-154127200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:154126400-154127200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:154126400-154127400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:154126400-154127400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:154126400-154127400	Genic enhancers	Primary B cells from cord blood	blood
42	chr1:154126400-154127600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr1:154126400-154127600	Genic enhancers	Spleen	Spleen
44	chr1:154126400-154127800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:154126400-154128600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:154126400-154128600	Strong transcription	Thymus	Thymus
47	chr1:154126400-154129600	Genic enhancers	K562	blood
48	chr1:154126400-154129600	Genic enhancers	NHLF	lung
49	chr1:154126400-154129800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:154126400-154129800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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