Variant report

Variant	rs12408129
Chromosome Location	chr1:214790796-214790797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214786142..214788737-chr1:214789658..214792373,2	K562	blood:
2	chr1:214788681..214791513-chr1:214794324..214796385,3	K562	blood:
3	chr1:214774746..214778356-chr1:214788014..214793089,5	K562	blood:
4	chr1:214785055..214788737-chr1:214790332..214794302,7	K562	blood:

Variant related genes	Relation type
ENSG00000117724	Chromatin interaction
ENSG00000224584	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10494983	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10494984	0.97[AMR][1000 genomes]
rs11120372	0.97[AMR][1000 genomes]
rs11805402	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12058704	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12060367	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12067133	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12071057	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12081395	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12096879	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12097817	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12097854	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404854	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12405890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12405995	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12408153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12410075	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17023274	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023282	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023284	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17023293	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17023299	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023338	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023380	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17023384	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2070066	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280049	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2292377	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292378	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2292379	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2666840	0.81[ASN][1000 genomes]
rs3748692	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3748695	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3748696	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3748698	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3790646	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790647	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790648	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3790649	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3795514	0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3795516	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795517	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795518	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795519	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795520	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795522	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795523	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3795524	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41303281	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58247244	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58724390	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59918378	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60944459	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61546198	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6669573	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS 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	7 gene(s)	inside rSNPs	diseases
2	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997864	chr1:214778658-214994142	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214777600-214800400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:214777600-214810800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:214777600-214838600	Weak transcription	Esophagus	oesophagus
4	chr1:214777800-214838400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:214778000-214839200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:214778200-214791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:214778200-214791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:214778200-214793000	Weak transcription	HSMM	muscle
9	chr1:214778200-214793600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:214778200-214793800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:214778200-214803600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:214778400-214794200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:214778600-214791200	Weak transcription	NHEK	skin
14	chr1:214778800-214794000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:214781200-214818000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:214781600-214791400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:214781800-214792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:214781800-214794000	Weak transcription	Fetal Stomach	stomach
19	chr1:214781800-214795800	Weak transcription	Fetal Intestine Small	intestine
20	chr1:214782000-214803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:214782800-214792800	Weak transcription	Thymus	Thymus
22	chr1:214782800-214794000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:214783200-214794000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:214783200-214817800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:214783400-214791200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:214783400-214793000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:214783400-214838800	Weak transcription	Fetal Kidney	kidney
28	chr1:214784600-214834000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:214784800-214791000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:214784800-214803600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:214784800-214807400	Weak transcription	Fetal Brain Female	brain
32	chr1:214785600-214819400	Strong transcription	K562	blood
33	chr1:214785600-214843800	Strong transcription	Fetal Thymus	thymus
34	chr1:214785800-214800600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:214786000-214794600	Weak transcription	Primary T cells from cord blood	blood
36	chr1:214786200-214843000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:214786600-214797200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:214786600-214800200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:214786600-214833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:214786600-214843200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:214786800-214800400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:214786800-214805200	Strong transcription	Dnd41	blood
43	chr1:214786800-214843800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:214787200-214798200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:214787600-214796600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:214787600-214842200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:214787800-214798600	Strong transcription	HepG2	liver
48	chr1:214787800-214800400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:214788000-214803800	Weak transcription	Placenta	Placenta
50	chr1:214788000-214810400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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