Variant report

Variant	rs1534439
Chromosome Location	chr6:145018139-145018140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13199226	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213354	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406045	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1590054	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2328598	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2328600	0.92[AMR][1000 genomes]
rs4895649	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896736	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570640	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570641	0.92[AMR][1000 genomes]
rs6924941	0.85[AMR][1000 genomes]
rs6927255	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740417	0.84[EUR][1000 genomes]
rs7758449	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765963	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7765968	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9373423	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9376842	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376843	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390189	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390197	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390200	0.88[AMR][1000 genomes]
rs9403587	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9484899	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
2	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1021098	chr6:145017386-145106441	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144981200-145031000	Weak transcription	Placenta	Placenta
2	chr6:144983000-145024600	Weak transcription	Fetal Kidney	kidney
3	chr6:144996600-145018400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:144996600-145052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:144999400-145025400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:145000800-145025400	Weak transcription	HSMM	muscle
7	chr6:145004400-145047000	Weak transcription	HSMMtube	muscle
8	chr6:145005000-145031000	Weak transcription	HUVEC	blood vessel
9	chr6:145008400-145021200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:145009000-145029600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:145009000-145047000	Weak transcription	Esophagus	oesophagus
12	chr6:145010400-145029600	Weak transcription	Aorta	Aorta
13	chr6:145010600-145047000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:145010800-145031000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:145010800-145031400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:145011000-145027800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:145011000-145052600	Weak transcription	Ovary	ovary
18	chr6:145011200-145029600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:145011200-145035200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr6:145011600-145021200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:145011600-145023000	Weak transcription	Fetal Heart	heart
22	chr6:145011800-145031000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:145011800-145065600	Weak transcription	Pancreas	Pancrea
24	chr6:145011800-145090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:145011800-145096600	Weak transcription	Thymus	Thymus
26	chr6:145012000-145020600	Weak transcription	Dnd41	blood
27	chr6:145012000-145021400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:145012000-145026200	Weak transcription	Left Ventricle	heart
29	chr6:145012000-145029400	Weak transcription	Lung	lung
30	chr6:145012000-145036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:145012000-145039200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:145012000-145047000	Weak transcription	Gastric	stomach
33	chr6:145012000-145055600	Weak transcription	Spleen	Spleen
34	chr6:145012400-145021200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:145012400-145053000	Weak transcription	Fetal Stomach	stomach
36	chr6:145012800-145023200	Weak transcription	Fetal Thymus	thymus
37	chr6:145013400-145019400	Weak transcription	Primary B cells from cord blood	blood
38	chr6:145013400-145022400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:145013600-145019600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr6:145013600-145021000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:145013600-145021200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:145013600-145021200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:145013600-145023000	Weak transcription	Adipose Nuclei	Adipose
44	chr6:145013800-145031200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:145014200-145021200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:145014200-145033600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:145014200-145047000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:145015600-145020200	Weak transcription	Fetal Intestine Small	intestine
49	chr6:145017200-145018200	Enhancers	Fetal Lung	lung
50	chr6:145017200-145018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links