Variant report

Variant	rs438298
Chromosome Location	chr6:5102523-5102524
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	chr6:5098062..5100879-chr6:5101823..5104582,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs127119	0.94[ASN][1000 genomes]
rs127120	0.94[ASN][1000 genomes]
rs127124	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs127125	0.81[ASN][1000 genomes]
rs200848	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs200849	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200850	0.87[ASN][1000 genomes]
rs200851	0.94[ASN][1000 genomes]
rs200863	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs364878	0.94[ASN][1000 genomes]
rs364886	0.93[CHB][hapmap]
rs365609	0.94[ASN][1000 genomes]
rs374733	0.92[ASN][1000 genomes]
rs375064	0.84[MEX][hapmap]
rs376334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs385315	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs386688	0.94[ASN][1000 genomes]
rs389691	0.94[ASN][1000 genomes]
rs389707	0.94[ASN][1000 genomes]
rs394683	0.94[ASN][1000 genomes]
rs394761	0.94[ASN][1000 genomes]
rs402103	0.94[ASN][1000 genomes]
rs402541	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs413219	0.94[ASN][1000 genomes]
rs421473	0.94[ASN][1000 genomes]
rs424493	0.94[ASN][1000 genomes]
rs428513	0.87[ASN][1000 genomes]
rs435175	0.93[ASN][1000 genomes]
rs435545	0.94[ASN][1000 genomes]
rs439091	0.94[ASN][1000 genomes]
rs441463	0.84[MEX][hapmap]
rs445204	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs449200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452658	0.94[ASN][1000 genomes]
rs455504	0.94[ASN][1000 genomes]
rs455803	0.81[ASN][1000 genomes]
rs457453	0.81[CHB][hapmap]
rs457759	0.92[CEU][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs457846	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs460551	0.92[ASN][1000 genomes]
rs461144	0.98[ASN][1000 genomes]
rs461698	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs462749	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs464606	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs464681	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs464863	0.81[ASN][1000 genomes]
rs466368	0.92[ASN][1000 genomes]
rs466837	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs587777	0.83[ASN][1000 genomes]
rs591481	0.84[MEX][hapmap]
rs683261	0.94[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs85204	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs9606	0.90[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs438298	C6orf149	cis	multi-tissue	Pritchard
rs438298	PIP5K1P1	cis	cerebellum	SCAN
rs438298	TUBB2B	cis	cerebellum	SCAN
rs438298	LYRM4	cis	parietal	SCAN
rs438298	LYRM4	cis	multi-tissue	Pritchard
rs438298	LYRM4	cis	cerebellum	SCAN

Chromatin state (count:25 , 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	chr6:5095400-5106800	Weak transcription	Fetal Stomach	stomach
5	chr6:5095800-5114200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:5096000-5103000	Weak transcription	HepG2	liver
7	chr6:5096000-5112200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:5097200-5108600	Weak transcription	HSMMtube	muscle
9	chr6:5097600-5112800	Weak transcription	K562	blood
10	chr6:5097800-5102800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:5098600-5105400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:5098600-5117000	Weak transcription	Fetal Brain Female	brain
13	chr6:5099000-5102800	Weak transcription	Left Ventricle	heart
14	chr6:5099000-5108400	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:5099000-5130000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:5099200-5102800	Weak transcription	Fetal Heart	heart
17	chr6:5099400-5109000	Weak transcription	Right Ventricle	heart
18	chr6:5100600-5109000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:5101800-5107400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:5101800-5132200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:5102200-5102600	Weak transcription	Primary T cells from cord blood	blood
22	chr6:5102200-5107200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:5102200-5107400	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:5102400-5102600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:5102400-5102800	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links