Variant report

Variant	rs7841648
Chromosome Location	chr8:61326183-61326184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:61326120-61326270	RPTEC	kidney:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61324950..61327634-chr8:61427769..61429933,3	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CA8-3	chr8:61326115-61326211	ENSG00000251396
2	lnc-CA8-3	chr8:61326115-61326489	ENSG00000251396
3	lnc-CA8-3	chr8:61326115-61326377	ENSG00000251396
4	lnc-CA8-3	chr8:61326115-61326377	NONHSAT126822

No data

Variant related genes	Relation type
ENSG00000251396	TF binding region
ENSG00000104388	Chromatin interaction
ENSG00000251396	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10087760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10092773	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10102945	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10504312	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11988766	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11988798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12548711	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1318227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552070	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1842388	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893277	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1893279	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1941467	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2012856	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2068587	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2155831	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471873	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6471877	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6471880	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6471881	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6982032	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6982404	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6986664	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6994192	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6998307	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6999822	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7001436	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7004236	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7005668	0.84[ASN][1000 genomes]
rs7814226	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7819947	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7824474	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7824671	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7828383	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7831106	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9785091	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7841648	RAB2A	Cis_1M	lymphoblastoid	RTeQTL
rs7841648	RP11-163N6.2	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61309000-61330000	Weak transcription	Right Atrium	heart
2	chr8:61324000-61327000	Enhancers	Fetal Heart	heart
3	chr8:61324800-61327000	Enhancers	Placenta	Placenta
4	chr8:61325000-61326600	Active TSS	Brain Anterior Caudate	brain
5	chr8:61325200-61326400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr8:61325200-61326400	Active TSS	Brain Angular Gyrus	brain
7	chr8:61325200-61326400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:61325200-61326600	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr8:61325200-61327000	Enhancers	Pancreas	Pancrea
10	chr8:61325200-61327200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:61325400-61326200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr8:61325400-61326200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr8:61325400-61326200	Enhancers	Lung	lung
14	chr8:61325400-61326400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:61325400-61326400	Enhancers	Right Ventricle	heart
16	chr8:61325400-61326600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr8:61325400-61326600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr8:61325400-61327200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:61325400-61327200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:61325600-61326200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr8:61325600-61326200	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr8:61325600-61326200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr8:61325600-61326200	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr8:61325600-61326200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr8:61325600-61326200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr8:61325600-61326200	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr8:61325600-61326400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr8:61325600-61326800	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr8:61325600-61327000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:61325600-61327000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:61325600-61327000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr8:61325600-61330200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:61325800-61326200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:61325800-61326800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:61326000-61326200	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr8:61326000-61326200	Bivalent Enhancer	Fetal Brain Male	brain
37	chr8:61326000-61326400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:61326000-61326400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr8:61326000-61326400	Active TSS	Brain Substantia Nigra	brain
40	chr8:61326000-61326400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
41	chr8:61326000-61326400	Bivalent Enhancer	Fetal Stomach	stomach
42	chr8:61326000-61326600	Flanking Bivalent TSS/Enh	NH-A	brain

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