Variant report

Variant	rs1295386
Chromosome Location	chr6:119667377-119667378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119648699..119654492-chr6:119662714..119668241,6	K562	blood:
2	chr6:119606943..119609052-chr6:119667352..119668942,2	K562	blood:
3	chr6:119469648..119470479-chr6:119666850..119667538,2	MCF-7	breast:
4	chr6:119649666..119652399-chr6:119665160..119668137,2	K562	blood:
5	chr6:119666514..119668057-chr6:120002574..120005085,2	MCF-7	breast:
6	chr6:119666964..119669354-chr6:119827597..119829582,2	K562	blood:
7	chr6:119658599..119660724-chr6:119666324..119670101,4	K562	blood:

Variant related genes	Relation type
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1104741	0.81[ASN][1000 genomes]
rs11153813	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11962211	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12211868	0.81[ASN][1000 genomes]
rs1295379	0.85[ASN][1000 genomes]
rs1295390	0.85[ASN][1000 genomes]
rs1295392	0.90[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs1298630	0.80[ASN][1000 genomes]
rs1797064	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs195046	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs195051	0.84[ASN][1000 genomes]
rs195062	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs195063	0.89[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs195071	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs195076	0.86[ASN][1000 genomes]
rs195078	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs195079	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs195081	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs195083	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs195085	0.80[ASN][1000 genomes]
rs195086	0.89[ASN][1000 genomes]
rs195088	0.84[ASN][1000 genomes]
rs195091	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2299879	0.94[CHB][hapmap]
rs2299881	0.81[ASN][1000 genomes]
rs3778111	0.86[MKK][hapmap];0.82[YRI][hapmap]
rs4945633	0.83[ASN][1000 genomes]
rs4946409	0.90[ASN][1000 genomes]
rs6569063	0.83[ASN][1000 genomes]
rs6569074	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6569075	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921356	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6924723	0.88[ASN][1000 genomes]
rs7757317	0.82[LWK][hapmap]
rs7765368	0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs7773367	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9320684	0.83[ASN][1000 genomes]
rs9387646	0.81[ASN][1000 genomes]
rs9489654	0.84[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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1295386	ASF1A	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119636200-119667400	Weak transcription	Right Ventricle	heart
3	chr6:119636200-119667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:119641400-119668200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:119645000-119668200	Weak transcription	Aorta	Aorta
6	chr6:119648200-119668000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:119648200-119668000	Weak transcription	Esophagus	oesophagus
8	chr6:119651000-119667400	Weak transcription	Fetal Stomach	stomach
9	chr6:119652200-119667600	Weak transcription	Thymus	Thymus
10	chr6:119652200-119667600	Weak transcription	NHLF	lung
11	chr6:119653200-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:119653200-119667800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:119657800-119667600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:119658000-119667400	Weak transcription	NHEK	skin
15	chr6:119658800-119667800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:119660800-119667600	Weak transcription	Fetal Brain Male	brain
17	chr6:119661200-119668000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:119661400-119668000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:119661600-119667800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:119661600-119667800	Transcr. at gene 5' and 3'	HepG2	liver
21	chr6:119662200-119669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:119662400-119667400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr6:119662600-119667400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:119662600-119667400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:119662600-119667600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:119662600-119667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:119662600-119667600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:119662600-119667600	Weak transcription	Left Ventricle	heart
29	chr6:119662600-119668600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:119662800-119667600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:119662800-119667600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:119662800-119667600	Weak transcription	Brain Angular Gyrus	brain
33	chr6:119662800-119667800	Weak transcription	Fetal Thymus	thymus
34	chr6:119663600-119667600	Weak transcription	Stomach Mucosa	stomach
35	chr6:119664000-119667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:119664000-119667600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:119664000-119667600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:119664000-119668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:119664400-119667600	Enhancers	Fetal Heart	heart
40	chr6:119664400-119668600	Transcr. at gene 5' and 3'	K562	blood
41	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
42	chr6:119665000-119667400	Weak transcription	Placenta	Placenta
43	chr6:119665000-119668600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
44	chr6:119665000-119669200	Weak transcription	Spleen	Spleen
45	chr6:119665200-119667600	Weak transcription	Fetal Lung	lung
46	chr6:119665200-119667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr6:119665600-119667600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:119665600-119667800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:119665600-119668600	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links