Variant report

Variant	rs642722
Chromosome Location	chr6:74270574-74270575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:74269217..74272384-chr6:74272449..74274240,3	K562	blood:
2	chr6:74269117..74271723-chr6:74288666..74291103,2	K562	blood:
3	chr6:74270566..74272311-chr6:74274568..74277117,2	K562	blood:
4	chr6:74228296..74231283-chr6:74268216..74270797,2	K562	blood:
5	chr6:74228889..74230513-chr6:74269068..74271779,2	K562	blood:
6	chr6:74269349..74272192-chr6:74274693..74276750,2	K562	blood:

Variant related genes	Relation type
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1390082	0.80[CEU][hapmap]
rs1874229	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4032321	0.80[CEU][hapmap]
rs4257823	0.86[AMR][1000 genomes]
rs4708062	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs473805	0.88[ASN][1000 genomes]
rs617464	0.80[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453679	0.80[EUR][1000 genomes]
rs780068	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9352005	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs9442924	0.80[CEU][hapmap]
rs9446917	0.80[CEU][hapmap];0.80[TSI][hapmap]

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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
9	nsv886159	chr6:74223153-74275405	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	159 gene(s)	inside rSNPs	diseases
10	nsv463153	chr6:74229258-74290291	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
11	nsv603693	chr6:74229258-74290291	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
12	nsv527357	chr6:74253266-74325403	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs642722	EEF1A1	cis	parietal	SCAN
rs642722	C6orf221	cis	cerebellum	SCAN
rs642722	EEF1A1	Cis_1M	lymphoblastoid	RTeQTL
rs642722	MTO1	Cis_1M	lymphoblastoid	RTeQTL
rs642722	EEF1A1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74266000-74275400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:74267200-74273800	Weak transcription	K562	blood
3	chr6:74268600-74274600	Weak transcription	HSMMtube	muscle
4	chr6:74268800-74275400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:74269000-74276800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:74269200-74275200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:74269400-74275400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:74269800-74270600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:74269800-74270600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:74269800-74271000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:74269800-74271000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:74270000-74270600	Enhancers	Duodenum Mucosa	Duodenum
13	chr6:74270000-74270600	Enhancers	NH-A	brain
14	chr6:74270000-74270800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:74270000-74270800	Enhancers	HUVEC	blood vessel
16	chr6:74270000-74271000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:74270000-74271000	Enhancers	Liver	Liver
18	chr6:74270200-74270600	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr6:74270200-74270600	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:74270200-74270600	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr6:74270200-74270600	Enhancers	Osteobl	bone
22	chr6:74270200-74270800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:74270200-74270800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:74270200-74270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:74270200-74270800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:74270200-74271200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:74270200-74271200	Enhancers	Brain Hippocampus Middle	brain
28	chr6:74270200-74271200	Enhancers	Fetal Lung	lung
29	chr6:74270200-74271200	Flanking Active TSS	GM12878-XiMat	blood
30	chr6:74270200-74271400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:74270400-74270600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr6:74270400-74270600	Enhancers	A549	lung
33	chr6:74270400-74270800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr6:74270400-74270800	Enhancers	Brain Angular Gyrus	brain
35	chr6:74270400-74271000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:74270400-74271200	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:74270400-74271200	Flanking Active TSS	HepG2	liver
38	chr6:74270400-74271200	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr6:74270400-74275200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:74270400-74275200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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