Variant report

Variant	rs4240339
Chromosome Location	chr4:148742314-148742315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148735688..148738679-chr4:148741409..148744100,2	MCF-7	breast:
2	chr4:148722709..148724828-chr4:148742107..148743929,2	MCF-7	breast:
3	chr4:148605030..148606697-chr4:148741931..148744308,2	MCF-7	breast:
4	chr4:148643022..148644770-chr4:148741282..148743199,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164169	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10003507	0.82[CEU][hapmap]
rs10004138	0.82[CEU][hapmap]
rs10004792	0.82[CEU][hapmap]
rs10004850	0.89[ASN][1000 genomes]
rs10005192	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10007231	0.86[ASN][1000 genomes]
rs10014696	0.82[CEU][hapmap]
rs10018820	0.82[CEU][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10018903	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10021936	0.85[ASN][1000 genomes]
rs10022691	0.85[ASN][1000 genomes]
rs10023057	0.85[CHD][hapmap]
rs10025684	0.88[ASN][1000 genomes]
rs10026985	0.82[CEU][hapmap]
rs10029385	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030358	0.82[CEU][hapmap]
rs10030513	0.88[ASN][1000 genomes]
rs10049932	0.82[CEU][hapmap]
rs10461235	0.85[CHD][hapmap]
rs10519917	0.85[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11099671	0.82[CEU][hapmap]
rs11099672	0.82[CEU][hapmap]
rs11724795	1.00[CEU][hapmap];0.88[CHD][hapmap]
rs11735412	0.82[CEU][hapmap]
rs11935450	0.85[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11935510	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs11935620	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs11940379	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs12331562	0.82[CEU][hapmap]
rs12509618	0.82[CEU][hapmap]
rs12513192	0.82[CEU][hapmap]
rs12641291	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12647314	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650219	1.00[CEU][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes]
rs13116821	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13129325	0.82[CEU][hapmap]
rs13129747	0.89[ASN][1000 genomes]
rs13434396	0.86[ASN][1000 genomes]
rs1369958	0.82[CEU][hapmap]
rs1436489	0.83[ASN][1000 genomes]
rs1436490	0.89[ASN][1000 genomes]
rs1469865	0.82[CHD][hapmap]
rs17023870	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs17023919	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023928	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17023995	0.89[ASN][1000 genomes]
rs17024037	0.82[CEU][hapmap]
rs17613979	0.82[CEU][hapmap]
rs17614025	0.82[CEU][hapmap]
rs17676080	0.82[CEU][hapmap]
rs2043644	1.00[CEU][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs28662484	0.87[ASN][1000 genomes]
rs35115631	0.89[ASN][1000 genomes]
rs3893175	0.82[CEU][hapmap]
rs3990920	0.82[CEU][hapmap]
rs4240338	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4240341	0.82[CEU][hapmap]
rs4419463	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4491995	0.82[CEU][hapmap]
rs4571312	0.82[CEU][hapmap]
rs66488204	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6818371	0.82[CEU][hapmap]
rs6839440	0.82[ASN][1000 genomes]
rs6840771	0.82[CEU][hapmap]
rs6843392	0.82[CEU][hapmap]
rs6846899	0.85[CHD][hapmap]
rs6856273	0.82[CEU][hapmap]
rs7654433	0.82[CHD][hapmap]
rs7655236	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7660508	0.82[CEU][hapmap]
rs7666127	0.82[CEU][hapmap];0.88[ASN][1000 genomes]
rs893022	1.00[CEU][hapmap]
rs893024	0.88[CHD][hapmap]
rs893033	0.82[CEU][hapmap]
rs9991741	0.82[CEU][hapmap]
rs9994650	0.82[CEU][hapmap]
rs9995896	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9995956	0.82[CEU][hapmap]
rs9996108	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9996209	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9997027	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148721800-148744200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:148732600-148744000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:148733200-148742400	Weak transcription	Fetal Intestine Small	intestine
4	chr4:148734000-148742800	Weak transcription	Fetal Lung	lung
5	chr4:148734600-148761000	Weak transcription	Fetal Kidney	kidney
6	chr4:148735800-148742800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:148737000-148747200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:148737200-148758200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:148737400-148742400	Weak transcription	Small Intestine	intestine
10	chr4:148737600-148742400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:148737600-148742400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:148737600-148742600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr4:148737600-148742800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:148737600-148742800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:148737600-148746800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:148737600-148747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:148737600-148747000	Weak transcription	Gastric	stomach
18	chr4:148737600-148750400	Weak transcription	Lung	lung
19	chr4:148737600-148751000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:148737800-148742400	Weak transcription	Fetal Stomach	stomach
21	chr4:148737800-148742400	Weak transcription	Fetal Thymus	thymus
22	chr4:148737800-148751400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr4:148737800-148755400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:148737800-148757000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:148737800-148782200	Weak transcription	Thymus	Thymus
26	chr4:148738600-148750400	Weak transcription	Placenta	Placenta
27	chr4:148738800-148742400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:148739000-148742400	Weak transcription	Adipose Nuclei	Adipose
29	chr4:148739200-148742400	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:148739800-148742400	Weak transcription	Fetal Heart	heart
31	chr4:148741000-148744200	Enhancers	Stomach Smooth Muscle	stomach
32	chr4:148741000-148744600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:148741200-148743400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:148741200-148744200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:148741400-148754000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:148741600-148743400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:148741800-148742400	Enhancers	NHEK	skin
38	chr4:148741800-148743600	Enhancers	HMEC	breast
39	chr4:148741800-148744400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:148742000-148742600	Enhancers	Fetal Muscle Trunk	muscle
41	chr4:148742000-148742600	Enhancers	Left Ventricle	heart
42	chr4:148742000-148744000	Enhancers	Ovary	ovary
43	chr4:148742000-148744400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:148742000-148744400	Enhancers	Right Atrium	heart
45	chr4:148742000-148744400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr4:148742000-148744600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:148742000-148745000	Enhancers	Fetal Muscle Leg	muscle
48	chr4:148742000-148745000	Enhancers	Psoas Muscle	Psoas
49	chr4:148742200-148742600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr4:148742200-148742600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links