Variant report

Variant	rs4353905
Chromosome Location	chr4:110745938-110745939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110744505..110746809-chr4:110749659..110751838,2	K562	blood:
2	chr4:110736461..110738940-chr4:110744765..110747082,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10020617	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10022841	0.94[CEU][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10516559	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11098049	0.81[ASN][1000 genomes]
rs12498239	0.87[ASN][1000 genomes]
rs12500239	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504835	0.94[CHB][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508179	0.87[ASN][1000 genomes]
rs12510851	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12513108	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12643147	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12644142	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13109228	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13112387	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115969	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs13128244	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs13129185	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13140289	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]
rs13141065	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13150454	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1860130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2078040	0.94[CEU][hapmap];0.87[ASN][1000 genomes]
rs2347130	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs2347131	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs2347132	0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs2347133	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs34377477	0.83[EUR][1000 genomes]
rs34378309	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34706258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34717063	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34734592	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35426158	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36101562	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775961	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4422417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4610335	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698749	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698750	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698795	0.88[CEU][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs62324955	0.83[EUR][1000 genomes]
rs6814655	0.87[ASN][1000 genomes]
rs6814743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816185	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6841737	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs6842245	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6858351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7442158	0.89[EUR][1000 genomes]
rs7657133	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7678178	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7684459	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7698794	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993509	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4353905	GAR1	cis	parietal	SCAN
rs4353905	GAR1	cis	cerebellum	SCAN
rs4353905	RRH	cis	parietal	SCAN
rs4353905	CYP2U1	cis	parietal	SCAN
rs4353905	LRIT3	cis	cerebellum	SCAN
rs4353905	RRH	cis	cerebellum	SCAN
rs4353905	ENPEP	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
2	chr4:110737800-110746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110737800-110746600	Weak transcription	Esophagus	oesophagus
4	chr4:110737800-110748000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:110737800-110753200	Weak transcription	Lung	lung
6	chr4:110738000-110747200	Weak transcription	Gastric	stomach
7	chr4:110738000-110748400	Weak transcription	Small Intestine	intestine
8	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:110738200-110746400	Weak transcription	Colonic Mucosa	Colon
10	chr4:110738200-110747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:110738400-110748000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:110738400-110748000	Weak transcription	Ovary	ovary
13	chr4:110738400-110748400	Weak transcription	Right Ventricle	heart
14	chr4:110738400-110748600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:110738600-110746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:110738600-110747000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:110738600-110747600	Weak transcription	Fetal Heart	heart
19	chr4:110738600-110748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:110738800-110746800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:110738800-110746800	Strong transcription	Adipose Nuclei	Adipose
22	chr4:110738800-110747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:110738800-110747000	Strong transcription	Fetal Thymus	thymus
24	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:110738800-110747200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:110738800-110747200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:110738800-110747200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:110738800-110747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:110738800-110748600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:110739000-110746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:110739000-110746800	Strong transcription	HUVEC	blood vessel
33	chr4:110739000-110747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:110739000-110747000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:110739000-110747000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:110739000-110747000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:110739000-110747000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:110739000-110747000	Strong transcription	K562	blood
39	chr4:110739000-110747000	Strong transcription	Osteobl	bone
40	chr4:110739000-110748400	Weak transcription	Fetal Brain Male	brain
41	chr4:110739000-110749800	Weak transcription	NHLF	lung
42	chr4:110739200-110746800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:110739200-110747000	Strong transcription	Liver	Liver
44	chr4:110739200-110747200	Strong transcription	NH-A	brain
45	chr4:110739200-110748400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr4:110739200-110748600	Strong transcription	HSMM	muscle
47	chr4:110739400-110747000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:110739400-110747600	Strong transcription	Dnd41	blood
49	chr4:110739600-110746400	Strong transcription	Placenta	Placenta
50	chr4:110739600-110746800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links