Variant report

Variant	rs12138150
Chromosome Location	chr1:169098738-169098739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169074913..169078230-chr1:169098350..169100536,3	MCF-7	breast:
2	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:
3	chr1:169096516..169099051-chr1:169103916..169105981,2	K562	blood:
4	chr1:169098028..169100792-chr1:169101427..169102956,2	K562	blood:
5	chr1:169092696..169095785-chr1:169096212..169101951,6	MCF-7	breast:
6	chr1:169094197..169097461-chr1:169097543..169100801,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10081960	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.83[ASN][1000 genomes]
rs1200079	0.97[ASN][1000 genomes]
rs1200161	0.80[ASN][1000 genomes]
rs1200164	0.80[ASN][1000 genomes]
rs1208327	0.83[ASN][1000 genomes]
rs12086665	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137282	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145897	0.91[YRI][hapmap]
rs12731646	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12752748	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861990	0.97[ASN][1000 genomes]
rs17345107	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345170	0.90[YRI][hapmap]
rs17349222	0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349271	0.90[YRI][hapmap]
rs1829286	0.83[ASN][1000 genomes]
rs2179490	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420008	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35152438	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656178	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803315	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803316	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67450288	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520186	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7522760	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542713	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552323	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12138150	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
5	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
7	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:169089600-169101600	Genic enhancers	A549	lung
12	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:169091000-169102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:169091000-169102200	Strong transcription	HepG2	liver
17	chr1:169091000-169102800	Strong transcription	Hela-S3	cervix
18	chr1:169091200-169124600	Weak transcription	NHLF	lung
19	chr1:169091400-169102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:169091400-169103200	Strong transcription	Liver	Liver
21	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:169091600-169101200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:169091600-169102000	Weak transcription	Pancreas	Pancrea
24	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
25	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:169091600-169120600	Weak transcription	Lung	lung
27	chr1:169091800-169104200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
29	chr1:169092200-169102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:169092400-169106200	Weak transcription	Gastric	stomach
31	chr1:169092600-169103600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:169093200-169100800	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:169093200-169103200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:169093400-169099400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:169093400-169099400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:169093400-169102000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:169093400-169102000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:169093400-169102800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:169093600-169102200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:169093600-169102400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:169093800-169100600	Strong transcription	Fetal Intestine Large	intestine
42	chr1:169093800-169101600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:169093800-169102200	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:169093800-169102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:169093800-169102600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:169094000-169099000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:169094000-169099400	Strong transcription	Placenta	Placenta
48	chr1:169094000-169101600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:169094400-169101000	Strong transcription	Colonic Mucosa	Colon
50	chr1:169094600-169101000	Strong transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links