Variant report

Variant	rs13141065
Chromosome Location	chr4:110744366-110744367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:110744325-110744397	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr4:110744035-110744394	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:110744194-110744715	K562	blood:	n/a	n/a
4	POLR2A	chr4:110744173-110744485	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110735461..110738460-chr4:110741089..110745272,5	MCF-7	breast:
2	chr4:110623035..110625693-chr4:110742775..110745001,2	MCF-7	breast:

Variant related genes	Relation type
RRH	TF binding region
ENSG00000109534	Chromatin interaction
ENSG00000272795	Chromatin interaction
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10020617	0.95[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516559	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs11937249	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs12500239	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12504835	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12510851	0.91[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12513108	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643147	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12644142	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13107617	0.95[CHB][hapmap]
rs13109228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112387	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13115969	0.89[CEU][hapmap]
rs13128244	0.83[CEU][hapmap];0.89[TSI][hapmap]
rs13128301	0.95[CHB][hapmap]
rs13129185	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13140289	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13150454	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860130	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2078040	0.89[CEU][hapmap]
rs2347130	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2347131	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs2347132	0.83[CEU][hapmap];0.81[CHB][hapmap];0.90[TSI][hapmap]
rs2347133	0.83[CEU][hapmap]
rs34378309	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34706258	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34717063	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34734592	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35426158	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36101562	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353905	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4422417	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610335	0.94[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4698749	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698750	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4698795	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs6814743	0.94[CEU][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6816185	0.88[CEU][hapmap]
rs6841737	0.89[CEU][hapmap]
rs6842245	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6858351	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7442158	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7657133	0.94[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678178	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7684459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698794	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9993509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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
rs13141065	RRH	cis	parietal	SCAN
rs13141065	LRIT3	cis	cerebellum	SCAN
rs13141065	GAR1	cis	parietal	SCAN
rs13141065	ENPEP	cis	cerebellum	SCAN
rs13141065	CYP2U1	cis	parietal	SCAN
rs13141065	RRH	cis	cerebellum	SCAN
rs13141065	GAR1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110737600-110745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:110737600-110745800	Weak transcription	Spleen	Spleen
3	chr4:110737600-110770600	Weak transcription	Aorta	Aorta
4	chr4:110737800-110746400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:110737800-110746600	Weak transcription	Esophagus	oesophagus
6	chr4:110737800-110748000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:110737800-110753200	Weak transcription	Lung	lung
8	chr4:110738000-110747200	Weak transcription	Gastric	stomach
9	chr4:110738000-110748400	Weak transcription	Small Intestine	intestine
10	chr4:110738000-110760800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:110738200-110746400	Weak transcription	Colonic Mucosa	Colon
12	chr4:110738200-110747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:110738400-110748000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:110738400-110748000	Weak transcription	Ovary	ovary
15	chr4:110738400-110748400	Weak transcription	Right Ventricle	heart
16	chr4:110738400-110748600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:110738400-110757200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:110738600-110746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:110738600-110747000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:110738600-110747600	Weak transcription	Fetal Heart	heart
21	chr4:110738600-110748400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:110738800-110744600	Strong transcription	A549	lung
23	chr4:110738800-110746800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:110738800-110746800	Strong transcription	Adipose Nuclei	Adipose
25	chr4:110738800-110747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:110738800-110747000	Strong transcription	Fetal Thymus	thymus
27	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:110738800-110747000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:110738800-110747200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:110738800-110747200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:110738800-110747200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:110738800-110747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:110738800-110748600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:110739000-110744600	Strong transcription	NHEK	skin
35	chr4:110739000-110745800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr4:110739000-110746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:110739000-110746800	Strong transcription	HUVEC	blood vessel
38	chr4:110739000-110747000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:110739000-110747000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:110739000-110747000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:110739000-110747000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:110739000-110747000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:110739000-110747000	Strong transcription	K562	blood
44	chr4:110739000-110747000	Strong transcription	Osteobl	bone
45	chr4:110739000-110748400	Weak transcription	Fetal Brain Male	brain
46	chr4:110739000-110749800	Weak transcription	NHLF	lung
47	chr4:110739200-110746800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:110739200-110747000	Strong transcription	Liver	Liver
49	chr4:110739200-110747200	Strong transcription	NH-A	brain
50	chr4:110739200-110748400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links