Variant report

Variant	rs41411146
Chromosome Location	chr5:1826047-1826048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1824982..1826633-chr5:1882223..1884332,2	MCF-7	breast:
2	chr5:1824774..1826571-chr5:1836421..1838392,2	K562	blood:
3	chr5:1801086..1802656-chr5:1824054..1826100,2	MCF-7	breast:
4	chr5:1823993..1826824-chr5:1830176..1831799,2	K562	blood:
5	chr5:1824315..1827809-chr5:1864869..1867236,3	MCF-7	breast:
6	chr5:1823993..1826108-chr5:1830299..1832827,2	K562	blood:
7	chr5:1820025..1823818-chr5:1823864..1826357,3	K562	blood:
8	chr5:1818595..1823818-chr5:1824144..1826436,4	K562	blood:
9	chr5:1813864..1817727-chr5:1823867..1827166,3	MCF-7	breast:
10	chr5:1825659..1827441-chr5:1889600..1892524,2	MCF-7	breast:
11	chr5:1823492..1825147-chr5:1825325..1826849,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000113430	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1018120	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10447190	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10447191	1.00[ASN][1000 genomes]
rs11948846	1.00[ASN][1000 genomes]
rs11953620	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11959171	0.86[ASN][1000 genomes]
rs12515616	0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs13170104	0.87[ASN][1000 genomes]
rs13173081	0.85[CHB][hapmap]
rs13178976	0.94[ASN][1000 genomes]
rs1532272	0.82[ASW][hapmap]
rs2270826	0.86[ASN][1000 genomes]
rs3776147	0.86[ASN][1000 genomes]
rs3776148	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs3776150	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4975732	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4975735	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4975846	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs4975847	0.93[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4975850	0.97[ASN][1000 genomes]
rs4975854	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs58460883	0.83[ASN][1000 genomes]
rs67272124	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv461911	chr5:1820557-1855301	Strong transcription Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv596890	chr5:1820557-1855301	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
6	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
9	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
10	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
11	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:1808800-1826200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr5:1808800-1826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:1808800-1828800	Strong transcription	Dnd41	blood
15	chr5:1809400-1827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:1809800-1826800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:1809800-1828200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:1810000-1826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:1813600-1826600	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr5:1813600-1827000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:1816600-1828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:1817400-1826400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:1817800-1828000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:1818000-1828400	Weak transcription	Fetal Heart	heart
25	chr5:1819400-1826800	Strong transcription	Fetal Intestine Small	intestine
26	chr5:1819400-1827000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:1819400-1828000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:1819600-1826600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:1820000-1828800	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:1820200-1827000	Strong transcription	Aorta	Aorta
31	chr5:1820400-1826200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:1820400-1828000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:1820600-1828800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:1821000-1826200	Weak transcription	Psoas Muscle	Psoas
35	chr5:1821000-1828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:1821600-1828000	Weak transcription	GM12878-XiMat	blood
37	chr5:1821800-1827000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:1821800-1828400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:1821800-1831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:1821800-1832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:1822000-1826200	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:1822000-1827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:1822000-1830400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:1822200-1827000	Strong transcription	Fetal Stomach	stomach
45	chr5:1822200-1829000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:1822200-1830800	Weak transcription	HSMM	muscle
47	chr5:1822200-1831800	Weak transcription	HSMMtube	muscle
48	chr5:1822400-1826200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:1822400-1827600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:1822400-1828000	Strong transcription	Right Ventricle	heart

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