Variant report

Variant	rs2499729
Chromosome Location	chr6:34097551-34097552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34096880..34099579-chr6:34108497..34110851,2	K562	blood:
2	chr6:34094975..34100252-chr6:34102486..34107232,5	K562	blood:
3	chr6:34094252..34097973-chr6:34098153..34100669,3	K562	blood:
4	chr6:34080081..34083212-chr6:34095884..34099849,3	MCF-7	breast:
5	chr6:34034996..34037075-chr6:34097163..34099972,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221779	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1075482	0.91[JPT][hapmap]
rs1109654	0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11753413	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12205473	0.90[ASN][1000 genomes]
rs12525536	0.91[ASN][1000 genomes]
rs12528906	0.83[ASN][1000 genomes]
rs2029457	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2029459	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2029460	0.89[EUR][1000 genomes]
rs2029461	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2029462	0.96[EUR][1000 genomes]
rs2451337	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2451339	0.88[ASN][1000 genomes]
rs2499722	0.91[JPT][hapmap]
rs2499725	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2499726	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2499728	0.89[ASN][1000 genomes]
rs2499730	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2499732	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713739	0.92[ASN][1000 genomes]
rs4713740	0.91[JPT][hapmap]
rs4713741	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4713742	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4713743	0.94[ASN][1000 genomes]
rs6928019	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs923498	0.88[ASN][1000 genomes]
rs9368794	0.92[ASN][1000 genomes]
rs9380409	0.80[CEU][hapmap]
rs9394188	0.96[ASN][1000 genomes]
rs9394189	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34025000-34101800	Weak transcription	Right Atrium	heart
2	chr6:34095600-34100800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:34096600-34099400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr6:34097000-34099400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:34097000-34099400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:34097000-34099400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:34097000-34099400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr6:34097000-34099400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr6:34097000-34099600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:34097000-34100000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:34097000-34101000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:34097200-34097600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:34097200-34099400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:34097200-34099400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:34097200-34101000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links