Variant report

Variant	rs744102
Chromosome Location	chr6:34078463-34078464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:34078447-34078492	Pancreas_OC	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:34069851..34072638-chr6:34076441..34079307,2	MCF-7	breast:
2	chr6:34072071..34075419-chr6:34078119..34081173,3	K562	blood:

Variant related genes	Relation type
GRM4	TF binding region
ENSG00000124493	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1109654	0.89[CEU][hapmap];0.84[GIH][hapmap];0.85[EUR][1000 genomes]
rs11753413	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs12205473	0.82[EUR][1000 genomes]
rs12525536	0.83[EUR][1000 genomes]
rs1565357	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1873246	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2029457	0.89[JPT][hapmap]
rs2029459	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs2029460	0.80[ASN][1000 genomes]
rs2029461	0.90[JPT][hapmap]
rs2046821	0.88[ASN][1000 genomes]
rs2087492	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451337	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs2451339	0.89[EUR][1000 genomes]
rs2499720	0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2499722	0.81[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2499724	0.89[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2499725	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2499726	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2499728	0.85[EUR][1000 genomes]
rs2499730	0.80[GIH][hapmap]
rs4713739	0.81[EUR][1000 genomes]
rs4713740	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4713741	0.80[EUR][1000 genomes]
rs4713742	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs4713743	0.84[EUR][1000 genomes]
rs4713744	0.92[ASN][1000 genomes]
rs6457757	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6918514	0.92[ASN][1000 genomes]
rs6918977	0.92[ASN][1000 genomes]
rs730638	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs914813	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs923498	0.90[EUR][1000 genomes]
rs9368794	0.85[EUR][1000 genomes]
rs9394189	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916210	chr6:33804111-34144062	Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv462900	chr6:33932442-34195011	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv602843	chr6:33932442-34195011	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv432881	chr6:34026522-34213822	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv885779	chr6:34046131-34103662	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv885780	chr6:34050917-34131376	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv462902	chr6:34056726-34195011	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv602862	chr6:34056726-34195011	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	esv1794906	chr6:34067792-34082563	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3324528	chr6:34076874-34081272	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs744102	PI16	cis	cerebellum	SCAN
rs744102	C6orf227	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34025000-34101800	Weak transcription	Right Atrium	heart
2	chr6:34051400-34089000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:34067000-34097000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:34067200-34080600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:34067200-34089000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:34067400-34089000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:34071600-34081800	Weak transcription	Brain Anterior Caudate	brain
8	chr6:34077400-34080200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:34078200-34078800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:34078400-34078600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:34078400-34079200	Bivalent Enhancer	Fetal Brain Male	brain
12	chr6:34078400-34080800	Enhancers	Fetal Brain Female	brain

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