Variant report

Variant	rs260402
Chromosome Location	chr5:1881733-1881734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr5:1881148-1881740	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr5:1881470-1882532	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
3	POLR2A	chr5:1881594-1881945	MCF10A-Er-Src	breast:	n/a	n/a
4	CTBP2	chr5:1880471-1882435	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:1881479-1881780	MCF-7	breast:	n/a	n/a
6	MAX	chr5:1881127-1883194	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
7	TCF7L2	chr5:1881462-1882380	HCT-116	colon:	n/a	n/a
8	STAT3	chr5:1881598-1881840	MCF10A-Er-Src	breast:	n/a	chr5:1881744-1881756
9	YY1	chr5:1881101-1881835	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr5:1881155-1883265	H1-hESC	embryonic stem cell:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1882349-1882358
11	E2F6	chr5:1881272-1882651	H1-hESC	embryonic stem cell:	n/a	chr5:1882416-1882427 chr5:1882410-1882425 chr5:1881643-1881650 chr5:1881643-1881650 chr5:1882417-1882427 chr5:1882415-1882426 chr5:1881643-1881650 chr5:1882245-1882254 chr5:1882411-1882425
12	E2F6	chr5:1881274-1883118	H1-hESC	embryonic stem cell:	n/a	chr5:1882416-1882427 chr5:1882410-1882425 chr5:1881643-1881650 chr5:1881643-1881650 chr5:1882417-1882427 chr5:1882415-1882426 chr5:1881643-1881650 chr5:1882245-1882254 chr5:1882411-1882425
13	MAX	chr5:1881264-1884334	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
14	STAT3	chr5:1881469-1881741	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr5:1881552-1881807	MCF-7	breast:	n/a	n/a
16	POLR2A	chr5:1881436-1881739	HCT-116	colon:	n/a	n/a
17	MXI1	chr5:1881629-1881874	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr5:1881356-1884611	HCT-116	colon:	n/a	chr5:1882349-1882358 chr5:1882349-1882358 chr5:1882351-1882360 chr5:1884034-1884044 chr5:1882349-1882358
19	CHD2	chr5:1881242-1881816	H1-hESC	embryonic stem cell:	n/a	n/a
20	SP1	chr5:1881100-1881800	H1-hESC	embryonic stem cell:	n/a	chr5:1881742-1881751 chr5:1881742-1881752 chr5:1881467-1881478 chr5:1881738-1881752 chr5:1881451-1881462 chr5:1881748-1881757 chr5:1881434-1881445 chr5:1881748-1881758 chr5:1881402-1881413 chr5:1881741-1881753 chr5:1881744-1881758
21	POLR2A	chr5:1881359-1883606	HCT-116	colon:	n/a	n/a
22	BACH1	chr5:1881247-1881808	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr5:1881138-1882188	H1-hESC	embryonic stem cell:	n/a	chr5:1881798-1881811
24	JUND	chr5:1881270-1881902	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr5:1881513-1881752	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr5:1881481-1891348	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr5:1881471-1884378	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
2	chr5:1799841..1802509-chr5:1881368..1882987,2	K562	blood:
3	chr17:57923026..57925305-chr5:1880876..1883150,2	MCF-7	breast:
4	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:
5	chr5:1881475..1885354-chr5:1933918..1938503,4	MCF-7	breast:
6	chr5:1798942..1801341-chr5:1879541..1882987,3	K562	blood:

Variant related genes	Relation type
ENSG00000249116	TF binding region
IRX4	TF binding region
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000248994	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1032436	0.82[ASW][hapmap];0.81[LWK][hapmap]
rs10474731	0.81[ASN][1000 genomes]
rs1632597	0.85[ASN][1000 genomes]
rs1689718	0.96[ASN][1000 genomes]
rs6876836	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	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
6	nsv596892	chr5:1832240-1892759	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1019713	chr5:1833072-1884738	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv596893	chr5:1839498-1892759	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1018082	chr5:1849721-1884738	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv881470	chr5:1850563-1892759	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv881188	chr5:1852284-1892759	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv822962	chr5:1877770-1888630	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv16732	chr5:1880874-1883019	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv880886	chr5:1880891-1936443	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs260402	KIAA0947	cis	parietal	SCAN
rs260402	CLPTM1L	cis	cerebellum	SCAN
rs260402	IRX2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1876600-1882400	Weak transcription	Right Atrium	heart
2	chr5:1878600-1883000	Enhancers	Fetal Heart	heart
3	chr5:1879800-1885200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr5:1880400-1882200	Weak transcription	Pancreas	Pancrea
5	chr5:1880800-1881800	Weak transcription	Right Ventricle	heart
6	chr5:1880800-1882800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:1880800-1887800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr5:1881200-1885200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:1881400-1882000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:1881400-1882200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
11	chr5:1881400-1882400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:1881400-1884400	Bivalent Enhancer	Fetal Brain Male	brain
13	chr5:1881400-1886800	Bivalent Enhancer	Fetal Stomach	stomach
14	chr5:1881600-1881800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:1881600-1881800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:1881600-1881800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:1881600-1881800	Enhancers	Gastric	stomach
18	chr5:1881600-1881800	Enhancers	HMEC	breast
19	chr5:1881600-1882000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr5:1881600-1882000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:1881600-1882200	Enhancers	NHEK	skin
22	chr5:1881600-1882400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:1881600-1882400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:1881600-1882400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
25	chr5:1881600-1882400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:1881600-1882400	Bivalent Enhancer	Brain Germinal Matrix	brain
27	chr5:1881600-1882600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr5:1881600-1882600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:1881600-1882600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
30	chr5:1881600-1882800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:1881600-1882800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr5:1881600-1882800	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr5:1881600-1883000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:1881600-1883200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr5:1881600-1883200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr5:1881600-1883200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr5:1881600-1883800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:1881600-1884200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:1881600-1884600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr5:1881600-1885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--

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