Variant report

Variant	rs16864720
Chromosome Location	chr1:171612267-171612268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171611915..171613655-chr1:171683755..171685490,3	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs235502	1.00[CHB][hapmap]
rs34324629	0.82[AFR][1000 genomes]
rs41263718	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7545646	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv528322	chr1:171578532-171612267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv548191	chr1:171578532-171612267	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16864720	DPT	cis	parietal	SCAN
rs16864720	DCAF6	cis	cerebellum	SCAN
rs16864720	GPA33	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171605800-171614400	Weak transcription	Aorta	Aorta
2	chr1:171607800-171612400	Weak transcription	Adipose Nuclei	Adipose
3	chr1:171607800-171614000	Weak transcription	HepG2	liver
4	chr1:171609600-171612400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:171610000-171614000	Weak transcription	Spleen	Spleen
6	chr1:171610800-171614000	Weak transcription	Ovary	ovary
7	chr1:171610800-171614200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:171611000-171614000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:171611000-171614600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:171611200-171612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:171611200-171613800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:171611200-171614000	Weak transcription	Right Atrium	heart
13	chr1:171611200-171614400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:171611400-171614200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:171611400-171614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:171611400-171614400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:171611400-171614400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:171611400-171615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:171611600-171613600	Weak transcription	Liver	Liver
20	chr1:171611600-171614000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:171611600-171614200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:171611600-171614200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:171612200-171615000	Enhancers	Fetal Brain Male	brain

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