Variant report

Variant	rs4682479
Chromosome Location	chr3:112974641-112974642
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112854846..112855571-chr3:112974408..112974968,2	MCF-7	breast:
2	chr3:112929933..112932828-chr3:112972160..112974860,2	MCF-7	breast:
3	chr3:112854746..112855542-chr3:112974048..112975014,2	MCF-7	breast:
4	chr3:112970765..112972828-chr3:112974570..112977015,2	MCF-7	breast:
5	chr3:112973746..112975579-chr3:112978657..112981572,2	K562	blood:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10511323	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710894	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11717833	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11919134	0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs11928342	0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12485329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492273	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631733	0.90[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12638030	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860758	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16860787	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1875111	0.86[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2036282	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201971	0.83[AMR][1000 genomes]
rs34284771	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814398	0.95[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs3846046	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856718	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856719	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856720	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41271357	0.81[AMR][1000 genomes]
rs4682131	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682478	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682480	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682481	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682483	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55814436	0.81[AMR][1000 genomes]
rs73235142	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235143	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235153	0.82[AMR][1000 genomes]
rs7641410	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775222	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs999367	0.81[GIH][hapmap]

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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4682479	BOC	cis	parietal	SCAN
rs4682479	CD96	cis	cerebellum	SCAN
rs4682479	CRYL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112968600-112980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr3:112969600-112981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
6	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
7	chr3:112970200-112981000	Weak transcription	Gastric	stomach
8	chr3:112970200-112981000	Weak transcription	Pancreas	Pancrea
9	chr3:112971200-112975400	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr3:112971200-112978200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr3:112971400-112974800	Genic enhancers	Fetal Stomach	stomach
12	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:112972000-112980600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
15	chr3:112972600-112974800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:112972600-112975200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:112972600-112975600	Enhancers	HSMM	muscle
18	chr3:112972800-112976400	Enhancers	HSMMtube	muscle
19	chr3:112973200-112974800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:112973200-112975200	Enhancers	GM12878-XiMat	blood
21	chr3:112973400-112974800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:112973400-112976400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:112973400-112981800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:112973400-112982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:112973600-112974800	Weak transcription	Brain Substantia Nigra	brain
27	chr3:112973600-112977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:112973600-112978600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112973600-112978800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:112973600-112980400	Weak transcription	Brain Germinal Matrix	brain
31	chr3:112973600-112980400	Weak transcription	Fetal Kidney	kidney
32	chr3:112973600-112982000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:112973600-112983600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
36	chr3:112973800-112975200	Weak transcription	Left Ventricle	heart
37	chr3:112973800-112977800	Weak transcription	Adipose Nuclei	Adipose
38	chr3:112973800-112977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:112973800-112978600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:112973800-112979400	Weak transcription	Aorta	Aorta
41	chr3:112973800-112979400	Weak transcription	Esophagus	oesophagus
42	chr3:112973800-112981200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:112973800-112981800	Weak transcription	Psoas Muscle	Psoas
44	chr3:112973800-112983400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr3:112974000-112975000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:112974000-112975800	Strong transcription	Colon Smooth Muscle	Colon
47	chr3:112974000-112979400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:112974000-112979600	Weak transcription	Fetal Brain Female	brain
49	chr3:112974200-112975200	Weak transcription	Fetal Lung	lung
50	chr3:112974200-112976000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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