Variant report

Variant	rs402541
Chromosome Location	chr6:5106899-5106900
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5104035..5107580-chr6:5108547..5111180,4	K562	blood:

Variant related genes	Relation type
ENSG00000214113	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs127119	0.93[ASN][1000 genomes]
rs127120	0.93[ASN][1000 genomes]
rs127124	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs127125	0.82[ASN][1000 genomes]
rs200848	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200849	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200850	0.86[ASN][1000 genomes]
rs200851	0.93[ASN][1000 genomes]
rs200863	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs364878	0.93[ASN][1000 genomes]
rs364886	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs365609	0.93[ASN][1000 genomes]
rs374733	0.91[ASN][1000 genomes]
rs375064	0.88[MEX][hapmap]
rs376334	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs385315	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs386688	0.93[ASN][1000 genomes]
rs389691	0.93[ASN][1000 genomes]
rs389707	0.93[ASN][1000 genomes]
rs394252	0.80[MEX][hapmap]
rs394683	0.93[ASN][1000 genomes]
rs394761	0.93[ASN][1000 genomes]
rs402103	0.93[ASN][1000 genomes]
rs412628	0.81[ASN][1000 genomes]
rs413219	0.93[ASN][1000 genomes]
rs421473	0.93[ASN][1000 genomes]
rs423801	0.81[ASN][1000 genomes]
rs424493	0.93[ASN][1000 genomes]
rs428513	0.86[ASN][1000 genomes]
rs435175	0.95[ASN][1000 genomes]
rs435545	0.93[ASN][1000 genomes]
rs438298	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs439091	0.93[ASN][1000 genomes]
rs441463	0.88[MEX][hapmap]
rs445204	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs449200	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs452658	0.93[ASN][1000 genomes]
rs454984	0.81[ASN][1000 genomes]
rs455504	0.93[ASN][1000 genomes]
rs455803	0.82[ASN][1000 genomes]
rs457453	0.80[MEX][hapmap]
rs457759	1.00[CEU][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs457846	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs460551	0.96[ASN][1000 genomes]
rs461144	0.90[ASN][1000 genomes]
rs461698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs462749	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs464606	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs464681	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs464863	0.82[ASN][1000 genomes]
rs466368	0.96[ASN][1000 genomes]
rs466837	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs587777	0.84[ASN][1000 genomes]
rs591481	0.88[MEX][hapmap]
rs683261	0.88[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs85204	0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs9606	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017373	chr6:5066785-5128943	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv538112	chr6:5066785-5128943	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs402541	TUBB2B	cis	cerebellum	SCAN
rs402541	LYRM4	cis	Esophagus Muscularis	GTEx
rs402541	LYRM4	cis	multi-tissue	Pritchard
rs402541	LYRM4	cis	parietal	SCAN
rs402541	C6orf149	cis	lesional skin	skin_eQTL
rs402541	LYRM4	cis	cerebellum	SCAN
rs402541	PIP5K1P1	cis	cerebellum	SCAN
rs402541	C6orf149	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5091000-5108200	Weak transcription	Spleen	Spleen
2	chr6:5091000-5108800	Weak transcription	Right Atrium	heart
3	chr6:5091000-5109000	Weak transcription	Lung	lung
4	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:5096000-5112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:5097200-5108600	Weak transcription	HSMMtube	muscle
7	chr6:5097600-5112800	Weak transcription	K562	blood
8	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
9	chr6:5099000-5108400	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:5099400-5109000	Weak transcription	Right Ventricle	heart
12	chr6:5100600-5109000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:5101800-5107400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:5102200-5107200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:5102200-5107400	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:5102800-5110400	Weak transcription	Primary T cells from cord blood	blood
18	chr6:5102800-5111600	Weak transcription	Thymus	Thymus
19	chr6:5103000-5113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:5103200-5107400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:5103200-5113600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:5103200-5114000	Weak transcription	Dnd41	blood
23	chr6:5103200-5132800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:5103400-5108400	Weak transcription	Fetal Lung	lung
25	chr6:5103400-5110600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:5103800-5108800	Weak transcription	Left Ventricle	heart
27	chr6:5103800-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:5103800-5112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:5104000-5107600	Weak transcription	Pancreas	Pancrea
30	chr6:5104200-5112000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:5104200-5112200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:5104400-5108200	Weak transcription	Fetal Intestine Small	intestine
33	chr6:5104600-5109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:5105000-5107200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:5105000-5109400	Weak transcription	NHEK	skin
36	chr6:5105000-5113200	Strong transcription	HepG2	liver
37	chr6:5105200-5107400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:5105200-5107400	Weak transcription	Adipose Nuclei	Adipose
39	chr6:5105200-5115800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:5105200-5131400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:5105400-5107800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:5105800-5125600	Weak transcription	Ovary	ovary
43	chr6:5105800-5128200	Weak transcription	Primary B cells from cord blood	blood
44	chr6:5106400-5107400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:5106600-5107000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:5106600-5107600	Enhancers	Fetal Heart	heart
47	chr6:5106600-5108000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr6:5106800-5111800	Strong transcription	Fetal Stomach	stomach

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