Variant report

Variant	rs10490798
Chromosome Location	chr3:47328744-47328745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47321055..47325957-chr3:47326199..47329332,5	MCF-7	breast:
2	chr3:47327849..47330607-chr3:47409211..47411755,2	MCF-7	breast:
3	chr3:47328553..47330784-chr3:47354135..47356276,2	K562	blood:
4	chr3:47327276..47329634-chr3:47339647..47341726,2	MCF-7	breast:
5	chr3:47326087..47329023-chr3:47353816..47355413,2	K562	blood:

Variant related genes	Relation type
ENSG00000114648	Chromatin interaction
ENSG00000088727	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11130126	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11710121	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs11720439	0.82[ASN][1000 genomes]
rs11915074	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs11920853	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11921117	0.80[ASN][1000 genomes]
rs12490383	1.00[CEU][hapmap]
rs12631730	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs17080872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs17410853	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs2240796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs61386020	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767907	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]
rs6768221	0.83[ASN][1000 genomes]
rs9311403	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs9837343	0.90[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10490798	DHX30	cis	multi-tissue	Pritchard
rs10490798	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs10490798	H1FOO	trans	parietal	SCAN
rs10490798	FYCO1	cis	parietal	SCAN
rs10490798	SCAP	cis	parietal	SCAN
rs10490798	KLHL18	cis	normal skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47328800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:47325600-47328800	Weak transcription	Psoas Muscle	Psoas
4	chr3:47325600-47330400	Weak transcription	Colonic Mucosa	Colon
5	chr3:47325600-47331200	Weak transcription	Aorta	Aorta
6	chr3:47325600-47332000	Weak transcription	Esophagus	oesophagus
7	chr3:47325600-47334200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:47325600-47334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:47325600-47334400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:47325600-47344600	Weak transcription	Ovary	ovary
13	chr3:47325600-47367600	Weak transcription	A549	lung
14	chr3:47325800-47329000	Weak transcription	Fetal Intestine Small	intestine
15	chr3:47325800-47329800	Weak transcription	HMEC	breast
16	chr3:47325800-47331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:47325800-47331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:47325800-47332400	Weak transcription	Right Ventricle	heart
19	chr3:47325800-47332400	Weak transcription	NH-A	brain
20	chr3:47325800-47337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:47325800-47338000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:47325800-47338200	Weak transcription	HUVEC	blood vessel
23	chr3:47325800-47343800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
25	chr3:47326200-47329800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:47326200-47336400	Weak transcription	Lung	lung
27	chr3:47326200-47340800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:47326200-47344600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
30	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
31	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
32	chr3:47326200-47362200	Weak transcription	Gastric	stomach
33	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:47326400-47338200	Weak transcription	Stomach Mucosa	stomach
35	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:47326600-47329400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:47326600-47329600	Weak transcription	Fetal Brain Female	brain
38	chr3:47326600-47330400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:47326600-47334200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:47326600-47341200	Weak transcription	Placenta	Placenta
41	chr3:47326600-47351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:47326800-47333600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
44	chr3:47327000-47330200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:47327000-47330200	Weak transcription	Hela-S3	cervix
46	chr3:47327000-47332400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:47327000-47344400	Weak transcription	Brain Angular Gyrus	brain
48	chr3:47327200-47328800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:47327200-47328800	Enhancers	Spleen	Spleen
50	chr3:47327200-47336600	Strong transcription	Primary T cells from cord blood	blood

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