Variant report

Variant	rs12203759
Chromosome Location	chr6:88420106-88420107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88413588..88415968-chr6:88418558..88420511,2	MCF-7	breast:
2	chr6:88417828..88420650-chr6:88427328..88429817,3	MCF-7	breast:
3	chr6:88410597..88412864-chr6:88418588..88421461,2	MCF-7	breast:
4	chr6:88419645..88421479-chr6:88422577..88425566,3	MCF-7	breast:
5	chr6:88415419..88418408-chr6:88419849..88421936,2	K562	blood:
6	chr6:88410177..88411869-chr6:88419616..88422374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12190021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13200106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13202825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13203056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs13203790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13206536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13206957	1.00[JPT][hapmap]
rs13211833	1.00[ASN][1000 genomes]
rs13212076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13219631	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16879490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879528	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16879532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17504209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17504475	1.00[JPT][hapmap]
rs2307393	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs28381552	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs28752032	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080809	1.00[ASN][1000 genomes]
rs35326820	1.00[ASN][1000 genomes]
rs35440627	1.00[ASN][1000 genomes]
rs35607770	1.00[ASN][1000 genomes]
rs35965137	1.00[ASN][1000 genomes]
rs3734908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3763176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55686846	1.00[AMR][1000 genomes]
rs61432898	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62417757	1.00[ASN][1000 genomes]
rs62419465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62419466	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6900057	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6902069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6917424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6927654	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6927826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6929542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7738268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7744213	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap]
rs7749032	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7760919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7770458	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88412800-88432600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:88413000-88421600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:88413200-88424200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:88417200-88423400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:88417200-88424000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:88417400-88421800	Weak transcription	A549	lung
7	chr6:88417400-88424000	Weak transcription	HSMM	muscle
8	chr6:88418200-88424000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:88418400-88423800	Weak transcription	Osteobl	bone
10	chr6:88418600-88424000	Weak transcription	NHDF-Ad	bronchial
11	chr6:88419600-88420200	Enhancers	GM12878-XiMat	blood
12	chr6:88419600-88420200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr6:88419800-88420200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:88419800-88420200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:88419800-88420200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:88419800-88420400	Enhancers	K562	blood
17	chr6:88420000-88420400	Enhancers	Thymus	Thymus

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