Variant report

Variant	rs1200161
Chromosome Location	chr1:169117533-169117534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169075492..169077285-chr1:169114771..169117684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10081960	0.80[ASN][1000 genomes]
rs1018831	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753785	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800408	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800414	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800424	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800425	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10919105	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10919124	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1200076	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200077	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200083	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200085	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200164	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208370	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208371	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208375	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208377	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086665	0.80[ASN][1000 genomes]
rs12137282	0.80[ASN][1000 genomes]
rs12138150	0.80[ASN][1000 genomes]
rs12752748	0.80[ASN][1000 genomes]
rs1400839	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591733	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17345107	0.80[ASN][1000 genomes]
rs17349222	0.80[ASN][1000 genomes]
rs1829287	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1856303	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037250	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066000	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2152979	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2179490	0.80[ASN][1000 genomes]
rs2211017	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2420008	0.80[ASN][1000 genomes]
rs3766057	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4264046	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4454599	0.86[ASN][1000 genomes]
rs4656178	0.80[ASN][1000 genomes]
rs61803315	0.80[ASN][1000 genomes]
rs61803316	0.80[ASN][1000 genomes]
rs6662237	0.86[ASN][1000 genomes]
rs6691226	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7522760	0.80[ASN][1000 genomes]
rs7533257	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7542713	0.80[ASN][1000 genomes]
rs7552323	0.80[ASN][1000 genomes]
rs994986	0.80[EUR][1000 genomes];0.86[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1200161	NME7	cis	Artery Aorta	GTEx
rs1200161	NME7	cis	Artery Tibial	GTEx
rs1200161	NME7	cis	Nerve Tibial	GTEx
rs1200161	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1200161	NME7	cis	Esophagus Muscularis	GTEx
rs1200161	NME7	cis	Stomach	GTEx
rs1200161	NME7	cis	Thyroid	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091200-169124600	Weak transcription	NHLF	lung
2	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:169091600-169120600	Weak transcription	Lung	lung
4	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
5	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
6	chr1:169097000-169130000	Weak transcription	Ovary	ovary
7	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
10	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:169110400-169121800	Enhancers	Fetal Intestine Small	intestine
14	chr1:169112600-169118400	Enhancers	Stomach Mucosa	stomach
15	chr1:169112800-169120600	Weak transcription	Psoas Muscle	Psoas
16	chr1:169114800-169118200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr1:169115000-169120600	Enhancers	HepG2	liver
18	chr1:169115000-169121200	Enhancers	Duodenum Mucosa	Duodenum
19	chr1:169115000-169121800	Enhancers	Fetal Intestine Large	intestine
20	chr1:169115200-169118000	Enhancers	Liver	Liver
21	chr1:169115400-169117800	Weak transcription	K562	blood
22	chr1:169115400-169118000	Weak transcription	Small Intestine	intestine
23	chr1:169115800-169130400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:169116200-169118000	Enhancers	Pancreas	Pancrea
25	chr1:169116200-169130200	Weak transcription	Brain Anterior Caudate	brain
26	chr1:169116400-169126600	Weak transcription	Right Atrium	heart
27	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:169117000-169117800	Weak transcription	Fetal Kidney	kidney
29	chr1:169117200-169117600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:169117400-169118000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:169117400-169118000	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:169117400-169118000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr1:169117400-169118200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:169117400-169118200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:169117400-169118400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:169117400-169118400	Flanking Active TSS	A549	lung

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