Variant report

Variant	rs41347149
Chromosome Location	chr5:1826630-1826631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1824982..1826633-chr5:1882223..1884332,2	MCF-7	breast:
2	chr5:1823993..1826824-chr5:1830176..1831799,2	K562	blood:
3	chr5:1824315..1827809-chr5:1864869..1867236,3	MCF-7	breast:
4	chr5:1813864..1817727-chr5:1823867..1827166,3	MCF-7	breast:
5	chr5:1825659..1827441-chr5:1889600..1892524,2	MCF-7	breast:
6	chr5:1823492..1825147-chr5:1825325..1826849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10058270	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs10061246	1.00[CHB][hapmap]
rs10062133	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10070488	1.00[CEU][hapmap]
rs10078791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs10085011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs10085096	1.00[CHB][hapmap]
rs10085130	1.00[CHB][hapmap]
rs10474728	1.00[CEU][hapmap]
rs10475113	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10475114	1.00[CEU][hapmap]
rs11505119	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13361288	1.00[CEU][hapmap]
rs16901194	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6555013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs6861074	1.00[CEU][hapmap]
rs6862138	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6862520	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6864000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs6875087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs6891921	1.00[CHB][hapmap]
rs6899016	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap]
rs7718031	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7723998	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9312955	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	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
8	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
9	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
10	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
11	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:110 , 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	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
5	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
7	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:1808800-1826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:1808800-1828800	Strong transcription	Dnd41	blood
10	chr5:1809400-1827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:1809800-1826800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:1809800-1828200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:1813600-1827000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:1816600-1828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:1817800-1828000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:1818000-1828400	Weak transcription	Fetal Heart	heart
17	chr5:1819400-1826800	Strong transcription	Fetal Intestine Small	intestine
18	chr5:1819400-1827000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:1819400-1828000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr5:1820000-1828800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:1820200-1827000	Strong transcription	Aorta	Aorta
22	chr5:1820400-1828000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:1820600-1828800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:1821000-1828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:1821600-1828000	Weak transcription	GM12878-XiMat	blood
26	chr5:1821800-1827000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:1821800-1828400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:1821800-1831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:1821800-1832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:1822000-1827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:1822000-1830400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr5:1822200-1827000	Strong transcription	Fetal Stomach	stomach
33	chr5:1822200-1829000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:1822200-1830800	Weak transcription	HSMM	muscle
35	chr5:1822200-1831800	Weak transcription	HSMMtube	muscle
36	chr5:1822400-1827600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:1822400-1828000	Strong transcription	Right Ventricle	heart
38	chr5:1822400-1829400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:1822400-1830000	Weak transcription	Fetal Lung	lung
40	chr5:1822400-1831600	Weak transcription	HMEC	breast
41	chr5:1822400-1833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:1822600-1827800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:1822600-1829400	Weak transcription	NH-A	brain
44	chr5:1822600-1831600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:1822800-1827600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:1822800-1827800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:1822800-1828400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:1822800-1831200	Weak transcription	Osteobl	bone
49	chr5:1823000-1827800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:1823000-1830000	Weak transcription	K562	blood

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