Variant report

Variant	rs12138428
Chromosome Location	chr1:170505188-170505189
allele	G/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	chr1:170500588-170509342	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
2	chr1:170500034..170503040-chr1:170504550..170507151,5	K562	blood:

Variant related genes	Relation type
GORAB	TF binding region
ENSG00000231407	TF binding region
ENSG00000231407	Chromatin interaction
ENSG00000120370	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10800526	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919391	1.00[ASN][1000 genomes]
rs10919403	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919405	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919406	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919408	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919410	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919416	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10919417	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919421	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919423	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919424	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919426	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919430	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577004	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578119	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584810	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587811	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066718	1.00[ASN][1000 genomes]
rs12116863	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12116910	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120718	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120764	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123065	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124354	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124515	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126472	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128140	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128573	1.00[ASN][1000 genomes]
rs12130086	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130520	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132914	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134482	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135132	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135326	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137818	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138138	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139124	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140689	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141076	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12142689	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12145961	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402306	0.89[ASN][1000 genomes]
rs12402526	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405323	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409985	0.89[ASN][1000 genomes]
rs12724601	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333142	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412890	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537390	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591150	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350312	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1888173	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928716	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999523	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183372	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421326	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923079	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281371	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399219	1.00[ASN][1000 genomes]
rs4508077	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656776	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656781	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427253	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66639118	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667728	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675683	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696114	0.83[EUR][1000 genomes]
rs72709772	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709774	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511715	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519067	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170501800-170516000	Weak transcription	Spleen	Spleen
2	chr1:170502000-170506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:170502000-170506200	Weak transcription	Gastric	stomach
4	chr1:170502000-170508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:170502000-170515200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:170502000-170517200	Weak transcription	Esophagus	oesophagus
7	chr1:170502200-170508200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:170502200-170508400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:170502200-170508400	Weak transcription	Placenta	Placenta
10	chr1:170502200-170508400	Weak transcription	Fetal Thymus	thymus
11	chr1:170502200-170508400	Weak transcription	Thymus	Thymus
12	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:170502400-170506400	Weak transcription	Right Atrium	heart
14	chr1:170502400-170512200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:170502400-170514800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:170502600-170507200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:170502600-170507800	Weak transcription	Fetal Lung	lung
18	chr1:170502600-170508400	Weak transcription	Fetal Intestine Small	intestine
19	chr1:170502600-170508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:170502600-170508600	Weak transcription	Fetal Brain Female	brain
21	chr1:170502600-170509000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:170502600-170509800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:170502600-170510200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:170502600-170510200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:170502600-170511600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:170502600-170512000	Weak transcription	Aorta	Aorta
27	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
29	chr1:170502800-170505400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:170502800-170506000	Weak transcription	Stomach Mucosa	stomach
31	chr1:170502800-170506400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:170502800-170506400	Weak transcription	Psoas Muscle	Psoas
33	chr1:170502800-170506400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:170502800-170506800	Weak transcription	A549	lung
35	chr1:170502800-170507200	Weak transcription	HUVEC	blood vessel
36	chr1:170502800-170507600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr1:170502800-170507800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:170502800-170508200	Weak transcription	Fetal Stomach	stomach
39	chr1:170502800-170508400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:170502800-170508400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:170502800-170508400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:170502800-170508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:170502800-170508400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:170502800-170508800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:170502800-170509600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:170502800-170509600	Weak transcription	Brain Germinal Matrix	brain
48	chr1:170502800-170509800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:170502800-170512200	Weak transcription	Brain Anterior Caudate	brain
50	chr1:170502800-170513800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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