Variant report

Variant	rs4653564
Chromosome Location	chr1:224314814-224314815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224305830..224307987-chr1:224312983..224315689,3	K562	blood:
2	chr1:224313532..224316324-chr1:224319519..224321918,2	K562	blood:
3	chr1:224312506..224315473-chr1:224345868..224347563,2	K562	blood:
4	chr1:224312047..224314469-chr1:224314721..224316323,2	MCF-7	breast:
5	chr1:224313817..224316131-chr1:224691933..224694076,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10753454	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799478	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10799480	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916301	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916307	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916320	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916355	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916367	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916403	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916415	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11808787	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12038372	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12049583	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070670	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12076788	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12563153	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12730611	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13374070	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1492694	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16844819	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17560970	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1826421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011117	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2014782	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048997	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051105	0.86[ASN][1000 genomes]
rs2172361	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280291	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2404843	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2896985	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767730	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820482	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820483	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653563	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653568	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4653972	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653991	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653994	0.83[ASN][1000 genomes]
rs4653995	0.81[ASN][1000 genomes]
rs4654003	0.86[CHB][hapmap]
rs55664906	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55736782	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827699	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426143	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426169	0.89[ASN][1000 genomes]
rs6426178	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs66506223	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657467	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658494	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659234	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680651	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681673	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs6682292	0.86[CHB][hapmap]
rs6682551	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685405	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6688818	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690695	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698041	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6700284	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7511895	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7526252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7542293	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7546235	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908795	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs908801	0.86[CHB][hapmap]
rs997296	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873222	chr1:224292898-224335422	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4653564	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4653564	FBXO28	cis	multi-tissue	Pritchard
rs4653564	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224302800-224318200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:224302800-224318200	Weak transcription	Left Ventricle	heart
3	chr1:224302800-224318200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:224302800-224318400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:224302800-224319600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:224302800-224319600	Weak transcription	Esophagus	oesophagus
7	chr1:224302800-224319600	Weak transcription	Lung	lung
8	chr1:224302800-224319600	Weak transcription	Small Intestine	intestine
9	chr1:224302800-224320200	Weak transcription	Pancreas	Pancrea
10	chr1:224302800-224327200	Weak transcription	Aorta	Aorta
11	chr1:224303000-224315200	Weak transcription	Placenta	Placenta
12	chr1:224303000-224317800	Weak transcription	Ovary	ovary
13	chr1:224303000-224317800	Weak transcription	Thymus	Thymus
14	chr1:224303000-224318000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:224303000-224318200	Weak transcription	Colonic Mucosa	Colon
16	chr1:224303000-224329000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:224303000-224363400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:224303200-224315400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:224303200-224317800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:224303200-224318000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:224303200-224318000	Weak transcription	HSMMtube	muscle
22	chr1:224303600-224318000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:224304000-224315400	Weak transcription	NHLF	lung
24	chr1:224304000-224319600	Weak transcription	Fetal Stomach	stomach
25	chr1:224304200-224315400	Weak transcription	NHDF-Ad	bronchial
26	chr1:224304200-224317800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:224304200-224318200	Weak transcription	Fetal Heart	heart
28	chr1:224304400-224315000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:224304400-224315400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:224304400-224318200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:224304400-224318200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:224304400-224318200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:224304400-224318200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:224304400-224318200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:224304400-224320000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:224304600-224315400	Weak transcription	NH-A	brain
37	chr1:224304600-224316200	Weak transcription	HMEC	breast
38	chr1:224304600-224318000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:224304600-224318000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:224304600-224318000	Weak transcription	Brain Germinal Matrix	brain
41	chr1:224304600-224318000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:224304600-224318000	Weak transcription	Fetal Lung	lung
43	chr1:224304600-224318200	Weak transcription	Adipose Nuclei	Adipose
44	chr1:224304600-224318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:224304800-224318400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:224306200-224315000	Weak transcription	Liver	Liver
47	chr1:224306800-224317800	Weak transcription	Fetal Intestine Large	intestine
48	chr1:224307400-224315600	Weak transcription	HUVEC	blood vessel
49	chr1:224307400-224318200	Weak transcription	HSMM	muscle
50	chr1:224307600-224318000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links