Variant report

Variant	rs17354693
Chromosome Location	chr16:71663704-71663705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:71663580-71663730	WERI-Rb-1	eye:	n/a	chr16:71663682-71663700 chr16:71663684-71663705
2	CTCF	chr16:71663660-71663737	LNCaP	prostate:	n/a	chr16:71663682-71663700 chr16:71663684-71663705
3	MAX	chr16:71663591-71663954	MCF-7	breast:	n/a	n/a
4	GATA3	chr16:71663597-71663892	T-47D	breast:	n/a	n/a
5	YY1	chr16:71663587-71663758	GM12878	blood:	n/a	chr16:71663640-71663662 chr16:71663642-71663651

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71658952..71666464-chr16:71755738..71760832,8	MCF-7	breast:
2	chr16:71663311..71664033-chr16:71679280..71679891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260593	TF binding region
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10500562	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12149264	1.00[CEU][hapmap]
rs12444890	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12446333	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap]
rs12447033	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs12447672	0.84[EUR][1000 genomes]
rs12922775	0.91[CEU][hapmap]
rs12923781	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12924650	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap]
rs12927006	0.83[CEU][hapmap]
rs12927456	0.83[CEU][hapmap]
rs12927768	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12931191	0.91[CEU][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12933566	1.00[AFR][1000 genomes]
rs12935422	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17282500	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17345863	0.80[CEU][hapmap]
rs17347255	0.91[CEU][hapmap]
rs17355804	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17356206	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17356316	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34381861	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35390364	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs71403859	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7203606	0.91[CEU][hapmap];0.86[TSI][hapmap]
rs8051974	0.83[CEU][hapmap]
rs8063455	0.91[CEU][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv962218	chr16:71645202-71727606	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17354693	RP11-432I5.1	cis	Thyroid	GTEx
rs17354693	ATP6V0D1	cis	parietal	SCAN
rs17354693	TK2	cis	parietal	SCAN
rs17354693	NRN1L	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71661000-71671000	Weak transcription	Right Atrium	heart
2	chr16:71661000-71674200	Weak transcription	Gastric	stomach
3	chr16:71661200-71663800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr16:71661200-71664000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr16:71661200-71667000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:71662000-71663800	Enhancers	Pancreas	Pancrea
8	chr16:71662000-71674200	Weak transcription	Lung	lung
9	chr16:71662200-71665600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr16:71662400-71663800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:71662400-71664000	Enhancers	NHEK	skin
13	chr16:71662600-71663800	Genic enhancers	Fetal Intestine Large	intestine
14	chr16:71662600-71663800	Enhancers	Placenta	Placenta
15	chr16:71662600-71664000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr16:71662800-71663800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:71662800-71664200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:71662800-71673600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr16:71663000-71663800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:71663000-71663800	Enhancers	Fetal Muscle Trunk	muscle
22	chr16:71663000-71663800	Enhancers	HepG2	liver
23	chr16:71663000-71663800	Enhancers	HSMMtube	muscle
24	chr16:71663000-71666200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr16:71663000-71669600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr16:71663000-71670800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr16:71663200-71664000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr16:71663200-71664600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr16:71663200-71664600	Weak transcription	HMEC	breast
30	chr16:71663200-71666000	Weak transcription	Fetal Heart	heart
31	chr16:71663200-71666400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:71663200-71668600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr16:71663200-71670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:71663200-71670600	Weak transcription	Osteobl	bone
35	chr16:71663200-71670800	Weak transcription	Ovary	ovary
36	chr16:71663200-71671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr16:71663200-71673800	Weak transcription	Brain Hippocampus Middle	brain
38	chr16:71663200-71676800	Weak transcription	Fetal Kidney	kidney
39	chr16:71663400-71663800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
40	chr16:71663400-71664200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr16:71663400-71664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:71663400-71665800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr16:71663400-71668200	Weak transcription	Fetal Stomach	stomach
44	chr16:71663400-71668800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr16:71663400-71669200	Strong transcription	Fetal Intestine Small	intestine
46	chr16:71663400-71669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr16:71663400-71670000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr16:71663400-71674200	Weak transcription	Adipose Nuclei	Adipose
49	chr16:71663400-71674200	Weak transcription	Aorta	Aorta
50	chr16:71663400-71674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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