Variant report

Variant	rs16862091
Chromosome Location	chr1:169318164-169318165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:168572446..168573392-chr1:169317346..169318310,9	MCF-7	breast:
2	chr1:168605132..168606019-chr1:169317390..169318347,3	MCF-7	breast:
3	chr1:169317063..169319375-chr1:169454243..169457078,2	K562	blood:
4	chr1:168572459..168573424-chr1:169317442..169318283,3	MCF-7	breast:
5	chr1:168604062..168606034-chr1:169316647..169318325,2	MCF-7	breast:
6	chr1:168606300..168607332-chr1:169317339..169318501,5	MCF-7	breast:
7	chr1:168605217..168605845-chr1:169317745..169318328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16862089	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16862101	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57339033	1.00[AMR][1000 genomes]
rs57556667	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58003088	1.00[AMR][1000 genomes]
rs58149696	1.00[AMR][1000 genomes]
rs58775541	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58860567	1.00[AMR][1000 genomes]
rs6656776	1.00[AMR][1000 genomes]
rs6664612	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs6687062	1.00[AMR][1000 genomes]
rs73034687	1.00[AMR][1000 genomes]
rs73034701	1.00[AMR][1000 genomes]
rs73035376	1.00[AMR][1000 genomes]
rs73035381	1.00[AMR][1000 genomes]
rs73036804	1.00[AMR][1000 genomes]
rs73036820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036833	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036856	1.00[AMR][1000 genomes]
rs73036860	1.00[AMR][1000 genomes]
rs73041751	1.00[AMR][1000 genomes]
rs73041774	1.00[AMR][1000 genomes]
rs73051105	1.00[AMR][1000 genomes]
rs73051107	1.00[AMR][1000 genomes]
rs7417281	1.00[AMR][1000 genomes]
rs7532255	0.93[YRI][hapmap]
rs7532362	0.93[YRI][hapmap]
rs7534851	1.00[AMR][1000 genomes]

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	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS 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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
2	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
5	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:169309400-169336400	Weak transcription	Ovary	ovary
7	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:169314800-169318200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:169316400-169321800	Weak transcription	HUVEC	blood vessel
12	chr1:169316600-169318200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:169317000-169318200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:169317000-169318200	Enhancers	A549	lung
15	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
16	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:169317400-169318200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:169317800-169318600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
22	chr1:169318000-169318200	Enhancers	Fetal Intestine Large	intestine
23	chr1:169318000-169320800	Weak transcription	Liver	Liver
24	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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