Variant report

Variant	rs16824299
Chromosome Location	chr2:134154923-134154924
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	chr2:134154022..134156001-chr2:134158455..134161393,2	MCF-7	breast:
2	chr2:134148626..134150845-chr2:134154535..134156780,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222068	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10165601	0.88[CHB][hapmap];0.87[CHD][hapmap]
rs10171473	0.86[ASN][1000 genomes]
rs10175744	0.88[CHB][hapmap]
rs10180047	0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs10182656	0.85[ASN][1000 genomes]
rs10184630	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs10193087	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs10193730	0.83[ASN][1000 genomes]
rs10196395	0.83[ASN][1000 genomes]
rs10204436	0.83[ASN][1000 genomes]
rs10204527	0.83[ASN][1000 genomes]
rs10206474	0.86[ASN][1000 genomes]
rs11898252	0.85[ASN][1000 genomes]
rs12327930	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12328976	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs13392963	0.88[CHB][hapmap]
rs13396831	0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs13396930	0.86[ASN][1000 genomes]
rs13406057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13406354	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13407205	1.00[CHB][hapmap]
rs13407503	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13408835	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13411233	0.88[CHB][hapmap];0.87[CHD][hapmap]
rs13412956	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs13421761	0.82[ASN][1000 genomes]
rs13426157	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs13426681	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13432602	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs1369509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1369510	0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[ASN][1000 genomes]
rs1430168	0.88[CHB][hapmap]
rs1435556	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1435563	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1435564	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1435565	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1435566	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1561018	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16824301	0.91[ASN][1000 genomes]
rs16824303	0.91[ASN][1000 genomes]
rs16824511	0.88[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16824573	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs17745593	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17745851	0.82[ASN][1000 genomes]
rs17802295	0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs1898008	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2115864	0.88[CHB][hapmap]
rs2164326	0.86[ASN][1000 genomes]
rs2289075	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4588241	0.88[CHB][hapmap]
rs55788182	0.81[ASN][1000 genomes]
rs56410092	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62177669	0.88[ASN][1000 genomes]
rs62177672	0.82[ASN][1000 genomes]
rs7573164	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9287426	0.88[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]
rs990476	1.00[CHB][hapmap];0.86[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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv522324	chr2:134085665-134174032	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134149000-134155400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134153000-134155000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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