Variant report

Variant	rs979789
Chromosome Location	chr16:71666118-71666119
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	chr16:71658952..71666464-chr16:71755738..71760832,8	MCF-7	breast:
2	chr16:71572964..71574516-chr16:71664027..71666330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261513	Chromatin interaction
ENSG00000040199	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10083757	0.81[EUR][1000 genomes]
rs1035545	0.94[GIH][hapmap]
rs10500559	0.89[ASN][1000 genomes]
rs1058747	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs10775326	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11075890	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11075891	0.80[ASN][1000 genomes]
rs11075892	0.81[ASN][1000 genomes]
rs11075895	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11539980	0.92[GIH][hapmap];0.84[JPT][hapmap]
rs11643690	0.81[ASN][1000 genomes]
rs11647873	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11648240	0.93[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11648674	0.83[JPT][hapmap]
rs11859729	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11862798	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap]
rs11865683	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11866795	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs12051443	0.88[ASN][1000 genomes]
rs12051449	0.86[ASN][1000 genomes]
rs12051506	0.89[ASN][1000 genomes]
rs12149092	0.81[EUR][1000 genomes]
rs12149873	0.85[EUR][1000 genomes]
rs12444484	0.93[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12447856	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs12597065	0.89[JPT][hapmap]
rs12598902	0.94[JPT][hapmap]
rs12920243	0.89[JPT][hapmap]
rs12922859	0.87[EUR][1000 genomes]
rs12923644	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12927320	0.88[ASN][1000 genomes]
rs12928187	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12930206	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs12930418	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12932850	0.86[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs13380425	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1392483	0.89[JPT][hapmap]
rs1392487	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs1477386	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1582589	0.86[ASN][1000 genomes]
rs172649	0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs172650	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs2010428	0.84[EUR][1000 genomes]
rs2032920	0.82[ASN][1000 genomes]
rs2036338	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs2113222	0.80[ASN][1000 genomes]
rs2270829	0.87[EUR][1000 genomes]
rs2270830	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs2270831	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs2270832	0.87[JPT][hapmap]
rs2278031	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs2303224	0.88[ASN][1000 genomes]
rs2303225	0.89[JPT][hapmap]
rs2334879	0.85[ASN][1000 genomes]
rs2335716	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2432520	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs2432524	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs34764568	0.87[ASN][1000 genomes]
rs35939203	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3752681	0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs3829537	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3886515	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4444347	0.96[CEU][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs4788546	0.82[ASN][1000 genomes]
rs4788547	0.81[ASN][1000 genomes]
rs4788549	0.89[JPT][hapmap]
rs4788551	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs4788558	0.89[GIH][hapmap];0.89[JPT][hapmap]
rs4788809	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4788812	0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4788814	0.81[ASN][1000 genomes]
rs4788821	0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4788826	0.88[JPT][hapmap]
rs4788827	0.88[JPT][hapmap]
rs57997630	0.86[ASN][1000 genomes]
rs62053077	0.81[ASN][1000 genomes]
rs62053078	0.81[ASN][1000 genomes]
rs62053107	0.85[ASN][1000 genomes]
rs6499532	0.86[EUR][1000 genomes]
rs6499539	0.81[EUR][1000 genomes]
rs7185997	0.89[JPT][hapmap]
rs7186717	0.81[ASN][1000 genomes]
rs7186859	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7187877	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7188406	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7191593	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7192956	0.81[EUR][1000 genomes]
rs7195840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7196498	0.90[EUR][1000 genomes]
rs7201228	0.81[EUR][1000 genomes]
rs7201754	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7202288	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7203168	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7203216	0.90[EUR][1000 genomes]
rs7203231	0.85[CEU][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs7206039	0.81[ASN][1000 genomes]
rs8048057	0.94[GIH][hapmap];0.89[JPT][hapmap]
rs8048210	0.94[GIH][hapmap];0.89[JPT][hapmap]
rs8051760	0.81[EUR][1000 genomes]
rs8053070	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8056823	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8060867	0.89[JPT][hapmap]
rs8061613	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8061970	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8063535	0.90[EUR][1000 genomes]
rs8203	0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs918721	0.92[GIH][hapmap];0.83[JPT][hapmap]
rs951939	0.89[JPT][hapmap]
rs9921270	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs9925228	0.94[GIH][hapmap];0.89[JPT][hapmap]
rs9939455	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs9940217	0.89[JPT][hapmap]
rs9940707	0.92[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9940990	0.89[JPT][hapmap]

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
rs979789	SLC9A5	cis	cerebellum	SCAN
rs979789	CHTF8	cis	parietal	SCAN
rs979789	TMED6	cis	parietal	SCAN
rs979789	PHLPP2	cis	cerebellum	SCAN

Chromatin state (count:61 , 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	chr16:71661200-71667000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:71661800-71682000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr16:71662000-71674200	Weak transcription	Lung	lung
6	chr16:71662200-71671200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr16:71662600-71682000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr16:71662800-71673600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr16:71663000-71666200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr16:71663000-71669600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr16:71663000-71670800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr16:71663200-71666400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr16:71663200-71668600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:71663200-71670000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr16:71663200-71670600	Weak transcription	Osteobl	bone
16	chr16:71663200-71670800	Weak transcription	Ovary	ovary
17	chr16:71663200-71671000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr16:71663200-71673800	Weak transcription	Brain Hippocampus Middle	brain
19	chr16:71663200-71676800	Weak transcription	Fetal Kidney	kidney
20	chr16:71663400-71668200	Weak transcription	Fetal Stomach	stomach
21	chr16:71663400-71668800	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr16:71663400-71669200	Strong transcription	Fetal Intestine Small	intestine
23	chr16:71663400-71669400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:71663400-71670000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr16:71663400-71674200	Weak transcription	Adipose Nuclei	Adipose
26	chr16:71663400-71674200	Weak transcription	Aorta	Aorta
27	chr16:71663400-71674400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:71663400-71674400	Weak transcription	Esophagus	oesophagus
29	chr16:71663400-71678400	Weak transcription	Fetal Lung	lung
30	chr16:71663600-71668000	Weak transcription	Colonic Mucosa	Colon
31	chr16:71663600-71668600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr16:71663600-71686600	Weak transcription	Small Intestine	intestine
33	chr16:71663800-71667000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr16:71663800-71667800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr16:71663800-71667800	Weak transcription	Pancreas	Pancrea
36	chr16:71663800-71669800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr16:71663800-71673800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:71663800-71674200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:71663800-71680600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr16:71663800-71681400	Weak transcription	Left Ventricle	heart
41	chr16:71663800-71681400	Weak transcription	HepG2	liver
42	chr16:71664000-71667800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr16:71664000-71668000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:71664000-71669600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr16:71664000-71671000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:71664200-71667600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr16:71664200-71670400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:71664600-71682800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr16:71665000-71666200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr16:71665000-71671000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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