Variant report

Variant	rs1387647
Chromosome Location	chr3:99826942-99826943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99820099..99823148-chr3:99826094..99828977,3	MCF-7	breast:
2	chr3:99826432..99828172-chr3:99830393..99831997,2	K562	blood:
3	chr3:99826246..99828968-chr3:99829999..99832998,3	K562	blood:
4	chr3:99824566..99827105-chr3:99830597..99832323,2	MCF-7	breast:
5	chr3:99826567..99829453-chr3:99832757..99834371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10936008	0.80[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs12488245	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13059754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs2130369	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes]
rs35422475	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4577503	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs4928150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs4928151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928153	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4928230	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928235	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6798114	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs6802817	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806323	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808765	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs720688	0.86[AMR][1000 genomes]
rs7629487	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7636776	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7638900	0.80[TSI][hapmap]
rs7649349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs766778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793440	0.80[TSI][hapmap]
rs902159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289981	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9811920	0.92[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9814549	0.84[CEU][hapmap];0.80[GIH][hapmap];0.87[AMR][1000 genomes]
rs9837131	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9849632	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9865713	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1387647	EPHX1	trans	cerebellum	SCAN
rs1387647	OR5H6	cis	cerebellum	SCAN
rs1387647	SENP7	cis	parietal	SCAN
rs1387647	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99818000-99836600	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99821800-99827800	Enhancers	Stomach Smooth Muscle	stomach
4	chr3:99822400-99827000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:99822600-99827400	Enhancers	Duodenum Smooth Muscle	Duodenum
6	chr3:99822600-99828000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:99822800-99827600	Enhancers	Rectal Smooth Muscle	rectum
8	chr3:99822800-99827800	Enhancers	Fetal Intestine Large	intestine
9	chr3:99822800-99828000	Enhancers	Fetal Intestine Small	intestine
10	chr3:99823000-99828000	Enhancers	Colon Smooth Muscle	Colon
11	chr3:99823200-99827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:99823400-99828000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:99823600-99827400	Weak transcription	Gastric	stomach
14	chr3:99823600-99837200	Weak transcription	Pancreas	Pancrea
15	chr3:99823800-99827400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr3:99824400-99827800	Enhancers	Fetal Muscle Leg	muscle
17	chr3:99825200-99827600	Weak transcription	HSMMtube	muscle
18	chr3:99825200-99835000	Weak transcription	K562	blood
19	chr3:99825200-99840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:99825200-99844000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:99825200-99844200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:99825400-99827400	Weak transcription	Left Ventricle	heart
23	chr3:99825400-99829000	Weak transcription	Aorta	Aorta
24	chr3:99825600-99829000	Weak transcription	Right Atrium	heart
25	chr3:99825600-99841000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:99826000-99827200	Enhancers	Liver	Liver
27	chr3:99826000-99828000	Weak transcription	Psoas Muscle	Psoas
28	chr3:99826000-99833200	Weak transcription	Ovary	ovary
29	chr3:99826200-99827000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:99826200-99827200	Weak transcription	Hela-S3	cervix
31	chr3:99826200-99827400	Weak transcription	HepG2	liver
32	chr3:99826200-99838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:99826400-99827400	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:99826400-99827600	Weak transcription	Adipose Nuclei	Adipose
35	chr3:99826400-99827600	Weak transcription	Osteobl	bone
36	chr3:99826400-99832000	Weak transcription	Right Ventricle	heart
37	chr3:99826600-99827600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:99826800-99827200	Weak transcription	Fetal Kidney	kidney
40	chr3:99826800-99827400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links