Variant report

Variant	rs12128754
Chromosome Location	chr1:169825529-169825530
allele	A/G
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	chr1:169820501-169832002	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169821793..169826224-chr1:169827537..169831257,5	K562	blood:
2	chr1:169819577..169821810-chr1:169823722..169826124,2	K562	blood:
3	chr1:169823925..169827148-chr1:169828128..169831257,4	K562	blood:
4	chr1:169818930..169821400-chr1:169825229..169828152,2	K562	blood:

Variant related genes	Relation type
RN7SL333P	TF binding region
ENSG00000239494	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10159425	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10489170	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10489177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753796	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10753798	0.81[CHB][hapmap]
rs10800477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800478	0.81[CHB][hapmap]
rs10800482	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10919243	0.87[CHB][hapmap]
rs10919260	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes]
rs10919270	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs10919271	0.85[CEU][hapmap]
rs10919272	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs11804170	0.85[CEU][hapmap]
rs12049325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12127655	0.82[MEX][hapmap]
rs12135656	0.90[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12135826	0.97[EUR][1000 genomes]
rs12138675	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12401338	0.86[EUR][1000 genomes]
rs12760433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2143121	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272916	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35275808	0.85[EUR][1000 genomes]
rs3753311	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6427223	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427229	0.91[MEX][hapmap]
rs6658548	0.97[EUR][1000 genomes]
rs6670253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6679646	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6688806	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7533194	0.86[EUR][1000 genomes]
rs7552710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs882595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9787237	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9803717	0.81[CHB][hapmap]
rs9803860	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12128754	C1orf112	cis	cerebellum	SCAN
rs12128754	C1orf156	cis	cerebellum	SCAN
rs12128754	CREG1	cis	cerebellum	SCAN
rs12128754	LMX1A	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169786600-169841400	Strong transcription	Dnd41	blood
3	chr1:169791200-169841200	Strong transcription	Fetal Thymus	thymus
4	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
6	chr1:169808200-169841200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169808600-169827000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:169809200-169829400	Strong transcription	GM12878-XiMat	blood
9	chr1:169809200-169829600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:169810000-169828000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:169810400-169841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:169810600-169841200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:169810800-169841000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:169810800-169841200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:169811000-169841400	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr1:169811400-169825600	Strong transcription	HSMM	muscle
17	chr1:169811400-169827200	Strong transcription	K562	blood
18	chr1:169811600-169841200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:169811800-169827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:169811800-169836200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:169811800-169841400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:169812000-169840800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:169812800-169836400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:169813400-169841200	Strong transcription	Fetal Intestine Large	intestine
25	chr1:169814200-169838000	Strong transcription	Placenta	Placenta
26	chr1:169814400-169830400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:169814600-169843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:169814800-169836000	Strong transcription	Osteobl	bone
30	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:169815200-169843000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:169816600-169827800	Strong transcription	NHDF-Ad	bronchial
36	chr1:169817000-169826000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:169817800-169826000	Strong transcription	Thymus	Thymus
38	chr1:169817800-169829400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:169817800-169841000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:169818000-169826200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:169818000-169826200	Strong transcription	Ovary	ovary
43	chr1:169818000-169826400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr1:169818000-169832000	Strong transcription	Left Ventricle	heart
45	chr1:169818000-169838400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:169818000-169842800	Strong transcription	Primary B cells from cord blood	blood
47	chr1:169818200-169826000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:169818200-169841200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
50	chr1:169818600-169826600	Strong transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links