Variant report

Variant	rs6425605
Chromosome Location	chr1:180046670-180046671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:180046607-180046773	MCF-7	breast:	n/a	n/a
2	MYC	chr1:180046661-180046749	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180045161..180048156-chr1:180135974..180138865,2	MCF-7	breast:
2	chr1:180044342..180046715-chr1:180123815..180125802,2	MCF-7	breast:
3	chr1:180040343..180041864-chr1:180045399..180046954,2	K562	blood:

Variant related genes	Relation type
CEP350	TF binding region
ENSG00000116260	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10798731	1.00[ASN][1000 genomes]
rs10798733	1.00[ASN][1000 genomes]
rs10913911	1.00[ASN][1000 genomes]
rs10913912	1.00[ASN][1000 genomes]
rs10913913	1.00[ASN][1000 genomes]
rs10913915	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10913921	1.00[ASN][1000 genomes]
rs10913922	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913926	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913928	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913929	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579402	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589421	1.00[ASN][1000 genomes]
rs12117957	1.00[ASN][1000 genomes]
rs12119113	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120822	1.00[ASN][1000 genomes]
rs12124175	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12124336	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127248	1.00[ASN][1000 genomes]
rs12129928	1.00[ASN][1000 genomes]
rs12131995	1.00[ASN][1000 genomes]
rs12135952	1.00[ASN][1000 genomes]
rs12138251	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141545	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144757	1.00[ASN][1000 genomes]
rs12743903	1.00[ASN][1000 genomes]
rs12744192	1.00[ASN][1000 genomes]
rs3845390	1.00[ASN][1000 genomes]
rs4083553	1.00[ASN][1000 genomes]
rs4652477	1.00[ASN][1000 genomes]
rs4652478	1.00[ASN][1000 genomes]
rs55676403	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55882713	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56166206	1.00[ASN][1000 genomes]
rs58121876	1.00[ASN][1000 genomes]
rs59953116	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61605706	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693288	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702845	1.00[ASN][1000 genomes]
rs72710619	1.00[ASN][1000 genomes]
rs72710658	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521701	1.00[ASN][1000 genomes]
rs7521873	1.00[ASN][1000 genomes]
rs7522347	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533903	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538086	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7539784	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550093	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555418	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425484	0.89[EUR][1000 genomes]
rs9425862	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425864	1.00[ASN][1000 genomes]
rs9425869	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
13	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
14	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180009000-180069600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr1:180009200-180051800	Strong transcription	Fetal Thymus	thymus
9	chr1:180009200-180070000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:180010200-180052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:180010600-180051800	Strong transcription	Liver	Liver
12	chr1:180012800-180050400	Weak transcription	Stomach Mucosa	stomach
13	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:180016400-180049600	Weak transcription	NHEK	skin
15	chr1:180021400-180062200	Weak transcription	Fetal Heart	heart
16	chr1:180025000-180064800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:180027000-180050000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr1:180028600-180052200	Strong transcription	Dnd41	blood
19	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:180030000-180073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:180030400-180066600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:180031000-180052000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:180031400-180051800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:180031400-180056800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:180032000-180049800	Weak transcription	HMEC	breast
26	chr1:180032000-180063200	Weak transcription	NHLF	lung
27	chr1:180032600-180062400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:180033400-180047200	Weak transcription	Fetal Kidney	kidney
29	chr1:180034400-180062200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:180034600-180054400	Weak transcription	NH-A	brain
31	chr1:180034800-180062400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:180035000-180060200	Weak transcription	Gastric	stomach
33	chr1:180035000-180062200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:180035000-180062400	Weak transcription	Aorta	Aorta
35	chr1:180038400-180048800	Weak transcription	Fetal Brain Male	brain
36	chr1:180038400-180049600	Weak transcription	HUVEC	blood vessel
37	chr1:180038600-180050800	Strong transcription	Placenta	Placenta
38	chr1:180039000-180048000	Strong transcription	Fetal Intestine Large	intestine
39	chr1:180040000-180054400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:180040800-180047000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr1:180040800-180066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:180040800-180082200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr1:180041000-180051400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:180041000-180051800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:180041000-180051800	Strong transcription	Adipose Nuclei	Adipose
46	chr1:180041000-180051800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:180041600-180047800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:180041600-180053600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:180041800-180048000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:180041800-180048000	Strong transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links