Variant report

Variant	rs12731646
Chromosome Location	chr1:169090660-169090661
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	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10081960	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12086665	0.91[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12137282	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12138150	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12145897	0.90[YRI][hapmap]
rs12724494	0.85[CEU][hapmap]
rs12752748	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17345107	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17345170	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs17349222	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17349271	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs1892094	0.84[LWK][hapmap]
rs2179490	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2420008	0.91[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35152438	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656178	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61803315	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61803316	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67450288	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7520186	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7522760	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7542713	0.82[EUR][1000 genomes]
rs7552323	0.91[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12731646	NME7	cis	cerebellum	SCAN
rs12731646	DUSP27	cis	parietal	SCAN
rs12731646	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs12731646	NME7	cis	Artery Tibial	GTEx
rs12731646	TARS	trans	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169094600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169081000-169098200	Weak transcription	Small Intestine	intestine
4	chr1:169081200-169091800	Strong transcription	Fetal Brain Female	brain
5	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:169082400-169097400	Weak transcription	Fetal Thymus	thymus
7	chr1:169083600-169094600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:169084000-169094000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:169085400-169090800	Enhancers	NHLF	lung
11	chr1:169085400-169091000	Genic enhancers	HepG2	liver
12	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
13	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169085600-169090800	Weak transcription	Lung	lung
15	chr1:169085600-169091000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:169085600-169091200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:169085600-169091800	Genic enhancers	Rectal Mucosa Donor 31	rectum
18	chr1:169085600-169092400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:169085600-169094800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:169085600-169096600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:169085800-169090800	Weak transcription	Aorta	Aorta
22	chr1:169085800-169090800	Weak transcription	Spleen	Spleen
23	chr1:169085800-169091000	Weak transcription	Right Atrium	heart
24	chr1:169085800-169091400	Genic enhancers	Duodenum Mucosa	Duodenum
25	chr1:169085800-169094000	Weak transcription	Placenta	Placenta
26	chr1:169085800-169097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
28	chr1:169086200-169094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
31	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:169086600-169095400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:169086800-169091200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:169087000-169090800	Weak transcription	Gastric	stomach
38	chr1:169087000-169092600	Genic enhancers	Brain Hippocampus Middle	brain
39	chr1:169087000-169093800	Weak transcription	Dnd41	blood
40	chr1:169087200-169090800	Weak transcription	Esophagus	oesophagus
41	chr1:169087200-169090800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:169087600-169090800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:169087800-169091000	Weak transcription	Brain Germinal Matrix	brain
44	chr1:169087800-169091000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:169087800-169093600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:169087800-169094400	Weak transcription	Colonic Mucosa	Colon
47	chr1:169088000-169093800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:169088000-169093800	Weak transcription	Fetal Kidney	kidney
49	chr1:169088200-169090800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:169088400-169090800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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