Variant report

Variant	rs7761928
Chromosome Location	chr6:49520083-49520084
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49515017..49518306-chr6:49519777..49524035,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLYATL3-2	chr6:49520066-49520283	NONHSAT113058
2	lnc-GLYATL3-2	chr6:49520071-49520283	NONHSAT113059

Variant related genes	Relation type
ENSG00000197261	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10456625	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2396905	1.00[MEX][hapmap]
rs41273692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45551532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458697	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6905369	1.00[EUR][1000 genomes]
rs6912159	1.00[EUR][1000 genomes]
rs6912178	1.00[EUR][1000 genomes]
rs6912690	1.00[EUR][1000 genomes]
rs6919458	1.00[EUR][1000 genomes]
rs6925445	1.00[EUR][1000 genomes]
rs6927176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6927459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6939453	1.00[EUR][1000 genomes]
rs6939457	1.00[EUR][1000 genomes]
rs73431965	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73431999	1.00[EUR][1000 genomes]
rs73433806	1.00[EUR][1000 genomes]
rs73433809	1.00[EUR][1000 genomes]
rs73433816	1.00[EUR][1000 genomes]
rs7742891	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7758141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760893	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7761036	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9349495	1.00[EUR][1000 genomes]
rs9473590	1.00[EUR][1000 genomes]

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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49517800-49520200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:49517800-49520200	Active TSS	A549	lung
3	chr6:49518000-49520200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:49518000-49520200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:49518000-49520600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:49518000-49520600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:49518200-49520200	Active TSS	HMEC	breast
8	chr6:49518200-49520200	Active TSS	NHEK	skin
9	chr6:49518400-49520200	Active TSS	NH-A	brain
10	chr6:49518400-49520400	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:49519000-49521600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:49519200-49520200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:49519200-49520200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:49519200-49520200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:49519200-49520200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:49519200-49520400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:49519200-49520400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:49519200-49520400	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:49519200-49520400	Active TSS	Stomach Mucosa	stomach
20	chr6:49519200-49521400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:49519200-49524000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:49519400-49520200	Active TSS	Fetal Intestine Small	intestine
23	chr6:49519400-49520600	Active TSS	Fetal Stomach	stomach
24	chr6:49519400-49520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:49519400-49521200	Active TSS	Brain Anterior Caudate	brain
26	chr6:49519400-49526600	Enhancers	Hela-S3	cervix
27	chr6:49519400-49533600	Weak transcription	Pancreas	Pancrea
28	chr6:49519600-49520400	Active TSS	Adipose Nuclei	Adipose
29	chr6:49519800-49520200	Active TSS	HUVEC	blood vessel
30	chr6:49519800-49520400	Enhancers	Liver	Liver
31	chr6:49519800-49520400	Bivalent Enhancer	Brain Hippocampus Middle	brain
32	chr6:49519800-49520600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
33	chr6:49519800-49520600	Enhancers	Fetal Intestine Large	intestine
34	chr6:49519800-49521200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:49520000-49520200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr6:49520000-49520200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr6:49520000-49520200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:49520000-49520200	Weak transcription	GM12878-XiMat	blood
39	chr6:49520000-49520400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:49520000-49520600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
41	chr6:49520000-49520600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr6:49520000-49520600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:49520000-49520800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
44	chr6:49520000-49520800	Enhancers	Primary hematopoietic stem cells	blood
45	chr6:49520000-49521200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
46	chr6:49520000-49521400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:49520000-49521400	Active TSS	Duodenum Mucosa	Duodenum
48	chr6:49520000-49523800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:49520000-49524000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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