Variant report

Variant	rs12494864
Chromosome Location	chr3:112973240-112973241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112929933..112932828-chr3:112972160..112974860,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511323	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710894	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11717833	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11919134	0.87[MEX][hapmap]
rs11928342	0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12485329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491930	0.82[AMR][1000 genomes]
rs12492273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631733	0.90[CHB][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12638030	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[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];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16860787	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1875111	0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2036282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34284771	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814398	0.95[CHB][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3846046	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856718	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856719	0.89[EUR][1000 genomes]
rs3856720	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682131	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4682478	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682479	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]
rs4682480	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682481	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682483	0.82[EUR][1000 genomes]
rs73235142	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235143	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235147	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73235153	0.88[AMR][1000 genomes]
rs7620307	0.84[MEX][hapmap];0.83[AMR][1000 genomes]
rs7641410	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775222	0.93[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs999367	0.81[GIH][hapmap];0.84[MEX][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
rs12494864	CRYL1	trans	lymphoblastoid	seeQTL
rs12494864	BOC	cis	parietal	SCAN
rs12494864	CD96	cis	cerebellum	SCAN

Chromatin state (count:81 , 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	chr3:112966800-112973600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:112968600-112980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:112968800-112973400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:112969600-112973600	Weak transcription	Osteobl	bone
7	chr3:112969600-112981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
9	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
10	chr3:112970000-112973600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:112970000-112973600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:112970200-112973400	Weak transcription	Lung	lung
13	chr3:112970200-112981000	Weak transcription	Gastric	stomach
14	chr3:112970200-112981000	Weak transcription	Pancreas	Pancrea
15	chr3:112971200-112973600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:112971200-112975400	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr3:112971200-112978200	Genic enhancers	Fetal Muscle Leg	muscle
18	chr3:112971400-112973400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:112971400-112974800	Genic enhancers	Fetal Stomach	stomach
20	chr3:112971600-112974200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:112971600-112974600	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:112971800-112973400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:112971800-112973400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:112972000-112980600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:112972200-112974200	Enhancers	Fetal Lung	lung
27	chr3:112972200-112974200	Enhancers	Fetal Thymus	thymus
28	chr3:112972200-112974200	Enhancers	Ovary	ovary
29	chr3:112972400-112973400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112972400-112973400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:112972400-112973400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr3:112972400-112973400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:112972400-112973600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:112972400-112973600	Enhancers	Brain Germinal Matrix	brain
35	chr3:112972400-112973600	Enhancers	Fetal Kidney	kidney
36	chr3:112972400-112973800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:112972400-112974000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:112972400-112974000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr3:112972400-112974200	Enhancers	Fetal Brain Male	brain
40	chr3:112972400-112974400	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:112972400-112974600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
43	chr3:112972600-112973600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:112972600-112973800	Enhancers	Esophagus	oesophagus
45	chr3:112972600-112974000	Enhancers	Fetal Brain Female	brain
46	chr3:112972600-112974200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:112972600-112974200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:112972600-112974200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:112972600-112974200	Enhancers	Brain Cingulate Gyrus	brain
50	chr3:112972600-112974200	Enhancers	Monocytes-CD14+_RO01746	blood

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