Variant report

Variant	rs4650716
Chromosome Location	chr1:175128711-175128712
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175127835..175129941-chr1:175131932..175135022,3	K562	blood:
2	chr1:174991534..174994499-chr1:175127289..175129850,2	MCF-7	breast:
3	chr1:175124723..175127210-chr1:175127837..175131491,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120333	Chromatin interaction
ENSG00000206659	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1014554	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1014555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1057239	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057246	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057302	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs1057305	0.85[CHB][hapmap]
rs10753091	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10912901	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583687	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11585368	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12760073	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13373754	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374887	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1883102	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1894709	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285216	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285219	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285220	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2685	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34270511	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34370567	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4344281	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664840	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929	0.87[GIH][hapmap]
rs729675	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4650716	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:175121600-175130800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:175121800-175131200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:175122200-175132800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:175122200-175133400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:175122400-175129400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:175123200-175129600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:175123800-175129400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:175124000-175129000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
12	chr1:175124200-175129200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:175124400-175138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:175124600-175134600	Weak transcription	Small Intestine	intestine
15	chr1:175124800-175128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:175125000-175128800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:175125000-175128800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:175125000-175129000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:175125000-175129200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:175125000-175132000	Weak transcription	Fetal Lung	lung
21	chr1:175125400-175132400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:175125600-175129400	Weak transcription	Fetal Kidney	kidney
23	chr1:175125800-175128800	Weak transcription	Fetal Stomach	stomach
24	chr1:175126200-175129400	Weak transcription	Esophagus	oesophagus
25	chr1:175126800-175129000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:175126800-175129400	Weak transcription	Psoas Muscle	Psoas
27	chr1:175126800-175138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:175126800-175141800	Strong transcription	Primary B cells from cord blood	blood
29	chr1:175126800-175148800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:175127000-175135600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:175127000-175136200	Strong transcription	Thymus	Thymus
32	chr1:175127000-175136600	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:175127000-175136600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:175127000-175148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:175127200-175131400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:175127200-175136200	Strong transcription	Fetal Thymus	thymus
37	chr1:175127200-175137800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:175127200-175139000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr1:175127200-175139000	Strong transcription	Placenta	Placenta
40	chr1:175127200-175139200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:175127200-175147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:175127400-175128800	Weak transcription	HUVEC	blood vessel
43	chr1:175127400-175129800	Strong transcription	Fetal Muscle Leg	muscle
44	chr1:175127400-175134400	Weak transcription	Brain Substantia Nigra	brain
45	chr1:175127400-175137000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:175127400-175139200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:175127400-175144200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:175127400-175149400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:175127600-175129200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:175127600-175130600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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