Variant report

Variant	rs1638676
Chromosome Location	chr3:47327651-47327652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47321055..47325957-chr3:47326199..47329332,5	MCF-7	breast:
2	chr3:47327276..47329634-chr3:47339647..47341726,2	MCF-7	breast:
3	chr3:47326087..47329023-chr3:47353816..47355413,2	K562	blood:

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1038394	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs11130115	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs11130123	0.93[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11710013	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711824	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap]
rs11712445	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs11714294	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.85[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs11915074	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs13061071	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap]
rs13072802	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075233	0.85[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs13094438	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531875	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs17476234	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs2101247	0.92[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.93[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295428	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs295433	0.95[YRI][hapmap]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295449	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs295458	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs295461	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs3736177	0.96[CEU][hapmap]
rs4682852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.85[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap]
rs59689369	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767907	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs6768221	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs7636423	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807935	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807936	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878659	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9683033	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs9837343	0.81[CEU][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1638676	AMIGO3	cis	cerebellum	SCAN
rs1638676	CCDC12	cis	cerebellum	SCAN
rs1638676	C3orf75	cis	cerebellum	SCAN
rs1638676	PRKAR2A	cis	cerebellum	SCAN
rs1638676	NCKIPSD	cis	cerebellum	SCAN
rs1638676	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs1638676	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs1638676	SCAP	cis	parietal	SCAN
rs1638676	RTP3	cis	lesional skin	skin_eQTL
rs1638676	HYAL2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325000-47328400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:47325600-47328000	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:47325600-47328000	Weak transcription	Thymus	Thymus
5	chr3:47325600-47328200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:47325600-47328200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:47325600-47328400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:47325600-47328600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:47325600-47328600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:47325600-47328600	Enhancers	Colon Smooth Muscle	Colon
11	chr3:47325600-47328600	Weak transcription	HSMMtube	muscle
12	chr3:47325600-47328800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47325600-47328800	Weak transcription	Psoas Muscle	Psoas
14	chr3:47325600-47330400	Weak transcription	Colonic Mucosa	Colon
15	chr3:47325600-47331200	Weak transcription	Aorta	Aorta
16	chr3:47325600-47332000	Weak transcription	Esophagus	oesophagus
17	chr3:47325600-47334200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:47325600-47334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:47325600-47334400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:47325600-47344600	Weak transcription	Ovary	ovary
23	chr3:47325600-47367600	Weak transcription	A549	lung
24	chr3:47325800-47327800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:47325800-47328000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:47325800-47328000	Weak transcription	Osteobl	bone
27	chr3:47325800-47328200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:47325800-47328400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:47325800-47328400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:47325800-47328400	Enhancers	Primary B cells from cord blood	blood
31	chr3:47325800-47328400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:47325800-47328400	Enhancers	Adipose Nuclei	Adipose
33	chr3:47325800-47328400	Weak transcription	HSMM	muscle
34	chr3:47325800-47328400	Weak transcription	NHLF	lung
35	chr3:47325800-47328600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:47325800-47329000	Weak transcription	Fetal Intestine Small	intestine
37	chr3:47325800-47329800	Weak transcription	HMEC	breast
38	chr3:47325800-47331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:47325800-47331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:47325800-47332400	Weak transcription	Right Ventricle	heart
41	chr3:47325800-47332400	Weak transcription	NH-A	brain
42	chr3:47325800-47337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:47325800-47338000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:47325800-47338200	Weak transcription	HUVEC	blood vessel
45	chr3:47325800-47343800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
47	chr3:47326000-47328200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:47326200-47327800	Weak transcription	NHEK	skin
49	chr3:47326200-47328000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:47326200-47328200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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