Variant report

Variant	rs4656178
Chromosome Location	chr1:169107846-169107847
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	chr1:169076107..169077789-chr1:169105664..169108065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10081960	0.96[AMR][1000 genomes];0.97[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	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137282	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138150	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145897	0.85[AFR][1000 genomes]
rs12731646	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12752748	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861990	0.97[ASN][1000 genomes]
rs17345107	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345170	0.85[AFR][1000 genomes]
rs17349222	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17349271	0.85[AFR][1000 genomes]
rs1829286	0.83[ASN][1000 genomes]
rs2179490	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420008	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133990	0.85[AFR][1000 genomes]
rs35152438	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61803315	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803316	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67450288	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7520186	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7522760	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542713	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552323	1.00[AMR][1000 genomes];0.99[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
rs4656178	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091200-169124600	Weak transcription	NHLF	lung
2	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
3	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:169091600-169120600	Weak transcription	Lung	lung
5	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
6	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
7	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
8	chr1:169096800-169108600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:169097000-169130000	Weak transcription	Ovary	ovary
10	chr1:169097600-169108200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:169098800-169112200	Weak transcription	HSMM	muscle
12	chr1:169099400-169110400	Weak transcription	Osteobl	bone
13	chr1:169099400-169111200	Weak transcription	Aorta	Aorta
14	chr1:169099400-169112000	Weak transcription	Psoas Muscle	Psoas
15	chr1:169100000-169108600	Weak transcription	Fetal Intestine Small	intestine
16	chr1:169100800-169115000	Weak transcription	Small Intestine	intestine
17	chr1:169100800-169116200	Weak transcription	Fetal Kidney	kidney
18	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:169101000-169113800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
21	chr1:169101200-169108600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:169101200-169113800	Weak transcription	Brain Germinal Matrix	brain
23	chr1:169102000-169117400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:169102200-169108200	Weak transcription	HepG2	liver
25	chr1:169102400-169120600	Weak transcription	Left Ventricle	heart
26	chr1:169102800-169112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:169102800-169114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:169103000-169108200	Weak transcription	Fetal Intestine Large	intestine
29	chr1:169103200-169111200	Weak transcription	Liver	Liver
30	chr1:169103200-169116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:169103200-169116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:169103200-169117200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:169103200-169117400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:169103400-169109200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:169103400-169109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:169103400-169110600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:169103400-169110600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:169103600-169114000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:169104000-169110400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:169104200-169117400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:169104800-169120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:169105600-169108800	Weak transcription	Fetal Heart	heart
45	chr1:169105600-169113800	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:169106800-169108000	Weak transcription	A549	lung
47	chr1:169107800-169108800	Enhancers	GM12878-XiMat	blood

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