Variant report

Variant	rs1200160
Chromosome Location	chr1:169103195-169103196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169075106..169077398-chr1:169100554..169103661,3	MCF-7	breast:
2	chr1:169098857..169100595-chr1:169101188..169104374,3	MCF-7	breast:
3	chr1:169074264..169079348-chr1:169101298..169105278,6	MCF-7	breast:
4	chr1:169099109..169101213-chr1:169102148..169104233,2	MCF-7	breast:
5	chr1:168607280..168610004-chr1:169101747..169103897,2	MCF-7	breast:
6	chr1:168605193..168606024-chr1:169103173..169104078,2	MCF-7	breast:
7	chr1:169101598..169103432-chr1:169104990..169106712,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1040502	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10732287	1.00[CHB][hapmap]
rs10919064	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10919065	0.81[CEU][hapmap]
rs1200079	1.00[CHB][hapmap]
rs1208327	1.00[CHB][hapmap]
rs12086665	1.00[CHB][hapmap]
rs12128513	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128543	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137282	1.00[CHB][hapmap]
rs12752748	1.00[CHB][hapmap]
rs16861990	1.00[CHB][hapmap]
rs17345107	1.00[CHB][hapmap]
rs17349222	1.00[CHB][hapmap]
rs1892094	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2420008	1.00[CHB][hapmap]
rs2901029	0.81[CEU][hapmap]
rs3753292	0.88[CEU][hapmap]
rs3766039	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs3766042	0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656648	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427178	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517394	0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540067	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754549	0.88[ASN][1000 genomes]
rs754550	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs754551	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7552323	1.00[CHB][hapmap]
rs968304	0.80[CEU][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1200160	NME7	cis	Thyroid	GTEx
rs1200160	FMO2	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:169091200-169124600	Weak transcription	NHLF	lung
8	chr1:169091400-169103200	Strong transcription	Liver	Liver
9	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
11	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:169091600-169120600	Weak transcription	Lung	lung
13	chr1:169091800-169104200	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
15	chr1:169092400-169106200	Weak transcription	Gastric	stomach
16	chr1:169092600-169103600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:169093200-169103200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:169094600-169104000	Genic enhancers	Brain Hippocampus Middle	brain
19	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
20	chr1:169095800-169106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
22	chr1:169096800-169108600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:169097000-169130000	Weak transcription	Ovary	ovary
24	chr1:169097600-169108200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:169098200-169103400	Weak transcription	Fetal Brain Male	brain
26	chr1:169098200-169105000	Weak transcription	Right Ventricle	heart
27	chr1:169098800-169112200	Weak transcription	HSMM	muscle
28	chr1:169099000-169105000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:169099400-169103400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:169099400-169103400	Weak transcription	Placenta	Placenta
31	chr1:169099400-169103600	Weak transcription	HSMMtube	muscle
32	chr1:169099400-169110400	Weak transcription	Osteobl	bone
33	chr1:169099400-169111200	Weak transcription	Aorta	Aorta
34	chr1:169099400-169112000	Weak transcription	Psoas Muscle	Psoas
35	chr1:169100000-169108600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:169100800-169103400	Weak transcription	NH-A	brain
37	chr1:169100800-169103600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:169100800-169104600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
40	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
41	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:169101000-169103200	Weak transcription	Fetal Lung	lung
43	chr1:169101000-169105400	Weak transcription	Colonic Mucosa	Colon
44	chr1:169101000-169113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
46	chr1:169101200-169104400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:169101200-169104800	Weak transcription	Fetal Brain Female	brain
48	chr1:169101200-169108600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:169101200-169113800	Weak transcription	Brain Germinal Matrix	brain
50	chr1:169101400-169105800	Weak transcription	H1 Cell Line	embryonic stem cell

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