Variant report

Variant	rs6778728
Chromosome Location	chr3:159997061-159997062
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159995732..159998143-chr3:160015400..160017582,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10936199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1141023	0.82[CHB][hapmap]
rs16831149	0.86[YRI][hapmap];0.90[AFR][1000 genomes]
rs17236389	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs17236452	0.82[CHB][hapmap]
rs17236487	1.00[CHB][hapmap]
rs17826161	0.82[CHB][hapmap]
rs1953506	0.80[YRI][hapmap]
rs2152424	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3737214	0.84[EUR][1000 genomes]
rs4254702	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs4679879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679883	0.82[CHB][hapmap]
rs4680577	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs4680582	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs4680588	0.82[YRI][hapmap]
rs57843971	0.84[AFR][1000 genomes]
rs61269120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441314	0.89[YRI][hapmap]
rs6803828	0.80[YRI][hapmap]
rs73154542	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875248	0.88[AFR][1000 genomes]
rs7611130	0.89[YRI][hapmap]
rs7624902	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159971800-160009600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:159972600-160009400	Weak transcription	Fetal Stomach	stomach
4	chr3:159972800-159999000	Weak transcription	Aorta	Aorta
5	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
6	chr3:159974600-159999600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:159974800-160014400	Weak transcription	HSMM	muscle
8	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
11	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:159975600-160009600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:159977800-160014400	Weak transcription	NHDF-Ad	bronchial
16	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:159978800-159999000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:159978800-159999200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:159979000-160007800	Weak transcription	Liver	Liver
20	chr3:159979200-159999000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:159979600-160003400	Weak transcription	Hela-S3	cervix
22	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
23	chr3:159983000-160009400	Weak transcription	Pancreas	Pancrea
24	chr3:159983200-160000800	Weak transcription	Psoas Muscle	Psoas
25	chr3:159983400-160009400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:159983400-160014200	Weak transcription	HSMMtube	muscle
27	chr3:159983600-159999000	Weak transcription	Lung	lung
28	chr3:159983600-160020400	Weak transcription	Brain Germinal Matrix	brain
29	chr3:159983800-160001400	Weak transcription	Brain Substantia Nigra	brain
30	chr3:159984200-159998800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:159984600-160014600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:159985200-159997200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:159985800-159998800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:159985800-160011600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:159986000-160009200	Weak transcription	Thymus	Thymus
37	chr3:159986000-160009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:159986400-160009600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:159986400-160024800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:159987000-160014400	Weak transcription	NHLF	lung
41	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:159988800-160004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:159989400-160005200	Weak transcription	Adipose Nuclei	Adipose
44	chr3:159989800-159998400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:159990000-159999800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:159990200-159997800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:159990200-160005400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:159991000-160009400	Weak transcription	Gastric	stomach
49	chr3:159991000-160024800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:159991200-160000000	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links