Variant report

Variant	rs12027242
Chromosome Location	chr1:169349323-169349324
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169347200..169349790-chr1:169495385..169498063,2	MCF-7	breast:
2	chr1:169346482..169351680-chr1:169353078..169360345,13	K562	blood:
3	chr1:169341801..169344771-chr1:169346777..169350780,3	MCF-7	breast:
4	chr1:169346112..169350144-chr1:169384504..169386593,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10458395	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10458396	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10458397	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10800439	0.84[ASN][1000 genomes]
rs10800441	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10800446	0.87[ASN][1000 genomes]
rs10919154	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10919164	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10919167	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1112839	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12022776	0.86[ASN][1000 genomes]
rs12024897	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12026287	0.87[ASN][1000 genomes]
rs12034986	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12563090	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12564884	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1517748	0.84[ASN][1000 genomes]
rs1980198	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2003652	0.87[ASN][1000 genomes]
rs2003654	0.86[ASN][1000 genomes]
rs2014061	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2275299	0.84[ASN][1000 genomes]
rs3753303	0.87[ASN][1000 genomes]
rs3766096	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3818844	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4656670	0.84[ASN][1000 genomes]
rs6427186	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6427188	0.82[ASN][1000 genomes]
rs6427189	0.85[ASN][1000 genomes]
rs6660945	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6669741	0.87[ASN][1000 genomes]
rs6677410	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6696428	0.87[ASN][1000 genomes]
rs6696810	0.86[ASN][1000 genomes]
rs7516248	0.86[ASN][1000 genomes]
rs7528375	0.87[ASN][1000 genomes]
rs7528449	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7534737	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7537890	0.86[ASN][1000 genomes]
rs7539415	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs961404	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12027242	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169351200	Weak transcription	Lung	lung
2	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
3	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
4	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
5	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
6	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169338000-169365200	Weak transcription	Gastric	stomach
8	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
9	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
15	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
17	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
21	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
22	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
23	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:169339200-169351800	Weak transcription	Fetal Brain Male	brain
27	chr1:169339600-169351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:169340200-169356400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:169341000-169351400	Weak transcription	Brain Hippocampus Middle	brain
31	chr1:169341200-169349600	Weak transcription	GM12878-XiMat	blood
32	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:169342800-169351200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:169343000-169351400	Weak transcription	K562	blood
35	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:169344800-169359200	Strong transcription	HSMM	muscle
37	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:169345000-169355400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:169345200-169352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:169345200-169352400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:169345200-169353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:169345400-169353600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:169345400-169354000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:169345400-169366000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:169345600-169352400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:169345600-169352800	Strong transcription	HUVEC	blood vessel

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