Variant report

Variant	rs2301717
Chromosome Location	chr4:110619534-110619535
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110619077..110621790-chr4:110741632..110744275,3	K562	blood:
2	chr4:110619153..110620852-chr4:110735626..110738010,2	MCF-7	breast:
3	chr4:110354439..110356440-chr4:110619131..110621286,2	K562	blood:
4	chr4:110617659..110620407-chr4:110623274..110624827,2	MCF-7	breast:
5	chr4:110618563..110622220-chr4:110622548..110625878,6	K562	blood:
6	chr4:110611670..110613762-chr4:110619125..110621842,2	K562	blood:

Variant related genes	Relation type
ENSG00000273447	Chromatin interaction
ENSG00000247950	Chromatin interaction
ENSG00000109534	Chromatin interaction
ENSG00000138794	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000138802	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10004377	0.92[CEU][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11728699	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs11932526	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13107296	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13127878	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1541373	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17512351	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2237056	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3087494	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs3181187	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5030534	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5030535	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5030539	1.00[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6533449	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6831917	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6854876	0.82[CEU][hapmap]
rs7439493	0.89[ASW][hapmap];0.80[CEU][hapmap]
rs7674356	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682236	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7694620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992400	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9995011	0.89[ASW][hapmap];0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2301717	RRH	cis	cerebellum	SCAN
rs2301717	CASP6	cis	parietal	SCAN
rs2301717	LARP7	cis	parietal	SCAN
rs2301717	CASP6	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
2	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
3	chr4:110598800-110622800	Weak transcription	NHEK	skin
4	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
6	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
7	chr4:110605000-110622800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:110605200-110619800	Strong transcription	Dnd41	blood
9	chr4:110605600-110619800	Strong transcription	Fetal Thymus	thymus
10	chr4:110605600-110622800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:110605800-110622800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:110606400-110622800	Weak transcription	Hela-S3	cervix
13	chr4:110607200-110622800	Weak transcription	Fetal Brain Male	brain
14	chr4:110607800-110623200	Weak transcription	Brain Angular Gyrus	brain
15	chr4:110609000-110622800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:110609600-110623000	Weak transcription	A549	lung
17	chr4:110609800-110619600	Weak transcription	HepG2	liver
18	chr4:110609800-110623200	Weak transcription	Psoas Muscle	Psoas
19	chr4:110611000-110619600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:110611000-110623200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:110611200-110621600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:110611200-110623800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:110611400-110619800	Strong transcription	Fetal Lung	lung
24	chr4:110611600-110622600	Weak transcription	Fetal Heart	heart
25	chr4:110611600-110623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:110611800-110619600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:110612200-110622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:110612200-110623000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:110612400-110622800	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:110613000-110623200	Weak transcription	Brain Anterior Caudate	brain
31	chr4:110613200-110619800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:110613200-110622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:110613600-110620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:110613600-110622800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:110613800-110619600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:110613800-110622800	Weak transcription	NHDF-Ad	bronchial
37	chr4:110614200-110622600	Weak transcription	Brain Germinal Matrix	brain
38	chr4:110614200-110622800	Weak transcription	Right Ventricle	heart
39	chr4:110614200-110622800	Weak transcription	HMEC	breast
40	chr4:110614200-110623000	Weak transcription	NHLF	lung
41	chr4:110614200-110623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:110614400-110619800	Weak transcription	GM12878-XiMat	blood
43	chr4:110614400-110622800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:110614400-110622800	Weak transcription	Primary B cells from cord blood	blood
45	chr4:110614400-110622800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:110614400-110622800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:110614400-110622800	Weak transcription	Ovary	ovary
48	chr4:110614400-110622800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:110614400-110623000	Weak transcription	NH-A	brain
50	chr4:110614600-110622600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links