Variant report

Variant	rs3999408
Chromosome Location	chr12:121167387-121167388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121166188..121170592-chr12:121174629..121177744,4	K562	blood:
2	chr12:121161440..121165409-chr12:121166157..121170080,9	K562	blood:
3	chr12:121160022..121162940-chr12:121166052..121168172,2	MCF-7	breast:
4	chr12:121166233..121168963-chr12:121173743..121176239,2	K562	blood:
5	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
6	chr12:121164614..121167510-chr12:121171430..121173002,2	K562	blood:
7	chr12:121162994..121164820-chr12:121167005..121169099,2	MCF-7	breast:
8	chr12:121166701..121168249-chr12:121176996..121179213,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000122971	Chromatin interaction
ENSG00000256569	Chromatin interaction
ENSG00000265455	Chromatin interaction
ENSG00000175970	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10431386	0.81[CEU][hapmap]
rs12311479	0.81[ASN][1000 genomes]
rs12828810	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12829722	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1799958	0.93[EUR][1000 genomes]
rs2014355	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2066938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2239758	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2393778	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3021337	1.00[ASN][1000 genomes]
rs3021338	0.94[ASN][1000 genomes]
rs34030695	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34673751	0.94[EUR][1000 genomes]
rs34708625	0.93[EUR][1000 genomes]
rs34734847	0.90[ASN][1000 genomes]
rs35360964	0.88[ASN][1000 genomes]
rs35525135	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35599677	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35771722	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3752531	0.90[ASN][1000 genomes]
rs3916	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs55730005	0.90[ASN][1000 genomes]
rs56273049	0.90[ASN][1000 genomes]
rs57830821	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs60858026	0.87[ASN][1000 genomes]
rs71454661	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306541	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7313271	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv899558	chr12:121161589-121179939	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121164000-121177000	Weak transcription	Aorta	Aorta
2	chr12:121164200-121167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:121164200-121167400	Weak transcription	Brain Germinal Matrix	brain
4	chr12:121164200-121169800	Weak transcription	NH-A	brain
5	chr12:121164200-121170800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:121164200-121172600	Weak transcription	HSMMtube	muscle
7	chr12:121164200-121176400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:121164400-121167600	Weak transcription	Fetal Lung	lung
9	chr12:121164400-121168000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:121164400-121168200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:121164400-121168200	Weak transcription	Gastric	stomach
12	chr12:121164400-121168200	Weak transcription	Osteobl	bone
13	chr12:121164400-121168400	Weak transcription	Fetal Brain Male	brain
14	chr12:121164400-121169000	Weak transcription	Brain Angular Gyrus	brain
15	chr12:121164400-121169800	Weak transcription	HSMM	muscle
16	chr12:121164400-121170400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:121164400-121170400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:121164400-121170600	Weak transcription	NHDF-Ad	bronchial
19	chr12:121164400-121170800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:121164400-121170800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:121164400-121174800	Weak transcription	Esophagus	oesophagus
22	chr12:121164400-121176000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:121164400-121176600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:121164400-121177600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:121164400-121179600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:121164600-121167400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:121164600-121167600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:121164600-121167600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:121164600-121168000	Weak transcription	Fetal Brain Female	brain
30	chr12:121164600-121168200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:121164600-121168200	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:121164600-121168200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:121164600-121168600	Weak transcription	NHEK	skin
34	chr12:121164600-121169000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr12:121164600-121172600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:121164600-121177000	Weak transcription	Small Intestine	intestine
37	chr12:121164600-121177200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:121164600-121178000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:121164800-121167400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:121164800-121167600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:121164800-121168200	Weak transcription	Brain Substantia Nigra	brain
42	chr12:121164800-121169000	Strong transcription	Thymus	Thymus
43	chr12:121164800-121169200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:121164800-121169400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:121164800-121169400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:121164800-121169400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:121164800-121169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:121164800-121169400	Strong transcription	Fetal Stomach	stomach
49	chr12:121164800-121171600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:121164800-121173600	Weak transcription	GM12878-XiMat	blood

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