Variant report

Variant	rs2299445
Chromosome Location	chr7:117246315-117246316
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:58237960..58239522-chr7:117246298..117249075,2	MCF-7	breast:
2	7:115861595-115870968..7:117245849-117249704	H1-hESC	embryonic stem cell:	embryo
3	7:116544149-116547624..7:117245849-117249704	H1-hESC	embryonic stem cell:	embryo
4	7:117100350-117112126..7:117245849-117249704	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10487365	1.00[CEU][hapmap]
rs10953843	1.00[CEU][hapmap]
rs11769166	1.00[CEU][hapmap]
rs1208525	0.94[CHB][hapmap]
rs1208528	0.94[CHB][hapmap]
rs12534186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12535986	1.00[CEU][hapmap]
rs12672572	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13237279	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1469486	0.81[CEU][hapmap]
rs2106155	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs213976	0.89[ASN][1000 genomes]
rs213977	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs213983	0.86[ASN][1000 genomes]
rs213985	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs213987	1.00[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs214152	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs214167	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237721	1.00[CEU][hapmap]
rs2237725	1.00[CEU][hapmap]
rs2237726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2246450	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2254742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283054	1.00[CEU][hapmap]
rs2283058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2402229	0.94[CHB][hapmap]
rs34257228	0.83[EUR][1000 genomes]
rs35278595	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3808183	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4148682	1.00[CEU][hapmap]
rs4148698	1.00[CEU][hapmap]
rs4148703	1.00[CEU][hapmap]
rs4148709	1.00[CEU][hapmap]
rs4148713	0.81[EUR][1000 genomes]
rs4148714	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148724	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4373465	0.83[EUR][1000 genomes]
rs4730786	1.00[CEU][hapmap]
rs6975912	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6978581	0.89[CHB][hapmap]
rs6979185	1.00[CEU][hapmap]
rs7784537	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7793030	0.89[CHB][hapmap]
rs7797932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808424	1.00[CEU][hapmap]
rs975722	0.89[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889078	chr7:117135025-117246315	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv889082	chr7:117203417-117246315	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv889083	chr7:117203417-117256374	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv889084	chr7:117212723-117246315	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv889085	chr7:117214089-117246315	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv889086	chr7:117214089-117252873	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv889087	chr7:117226766-117246315	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117244000-117247200	Weak transcription	Gastric	stomach
2	chr7:117244200-117252600	Weak transcription	Dnd41	blood
3	chr7:117244200-117253200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:117244800-117246400	Enhancers	Fetal Intestine Large	intestine
5	chr7:117244800-117246400	Genic enhancers	Fetal Intestine Small	intestine
6	chr7:117244800-117246600	Enhancers	A549	lung
7	chr7:117245000-117246400	Enhancers	Liver	Liver
8	chr7:117245000-117246400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr7:117245000-117246600	Enhancers	Duodenum Mucosa	Duodenum
10	chr7:117245000-117252800	Weak transcription	Small Intestine	intestine
11	chr7:117245200-117294000	Weak transcription	Pancreas	Pancrea
12	chr7:117245800-117256600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:117246200-117246400	Enhancers	Sigmoid Colon	Sigmoid Colon

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