Variant report

Variant	rs2745599
Chromosome Location	chr6:1613686-1613687
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:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:1612494..1615565-chr6:2103145..2107069,5	MCF-7	breast:
2	chr6:1613450..1614402-chr6:1641238..1641879,5	MCF-7	breast:
3	chr6:1612762..1614490-chr6:1684651..1686337,2	MCF-7	breast:
4	chr6:1613601..1616757-chr6:1636130..1638960,3	MCF-7	breast:
5	chr6:1607121..1609914-chr6:1613223..1615033,2	K562	blood:
6	chr6:1610715..1613985-chr6:2196585..2199138,3	MCF-7	breast:
7	chr6:1613541..1614598-chr6:1641560..1642153,3	MCF-7	breast:
8	chr6:1611913..1614321-chr6:1833472..1836057,3	MCF-7	breast:
9	chr6:1613523..1614289-chr6:1838606..1839498,2	MCF-7	breast:
10	chr6:1612565..1615275-chr6:1837590..1839107,2	MCF-7	breast:
11	chr6:1613541..1614425-chr6:1641560..1642119,3	MCF-7	breast:
12	chr6:1612582..1614145-chr6:1846859..1849142,2	MCF-7	breast:
13	chr6:1612951..1615735-chr6:3066934..3068619,2	MCF-7	breast:
14	chr6:1613675..1614411-chr6:1641501..1642080,3	MCF-7	breast:
15	chr1:183441719..183444081-chr6:1612481..1614965,2	MCF-7	breast:
16	chr6:1612605..1614594-chr6:1617750..1620318,2	K562	blood:
17	chr6:1612642..1614747-chr6:1828037..1830665,2	MCF-7	breast:
18	chr6:1612577..1614591-chr6:1838798..1840944,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-3	chr6:1612577-1614127	NONHSAT106538

No data

Variant related genes	Relation type
ENSG00000116698	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2569880	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2745596	0.84[MKK][hapmap]
rs984253	1.00[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883376	chr6:1535043-1635082	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
14	nsv823394	chr6:1590091-1629146	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv883378	chr6:1593851-1623990	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	nsv883379	chr6:1593851-1628902	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
17	nsv823395	chr6:1595031-1629521	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
18	nsv883380	chr6:1595216-1621404	Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
19	nsv883381	chr6:1595216-1628902	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
20	nsv823396	chr6:1597359-1629106	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
21	nsv883382	chr6:1598942-1620037	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	nsv823397	chr6:1603867-1622264	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
23	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
24	esv3409241	chr6:1608853-1616151	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
25	esv3436874	chr6:1609353-1613751	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
26	nsv600807	chr6:1610884-1623990	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
27	esv3377457	chr6:1613478-1616526	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2745599	RPP40	cis	cerebellum	SCAN
rs2745599	SERPINB6	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1605600-1620800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:1609000-1615200	Active TSS	Right Atrium	heart
3	chr6:1609000-1615400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:1609200-1614400	Active TSS	A549	lung
5	chr6:1609400-1616000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:1609600-1614400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:1609600-1614800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:1609600-1616000	Active TSS	Hela-S3	cervix
9	chr6:1609800-1613800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:1609800-1613800	Active TSS	HUVEC	blood vessel
11	chr6:1609800-1614000	Active TSS	NHLF	lung
12	chr6:1609800-1614600	Active TSS	HMEC	breast
13	chr6:1610400-1614000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:1611000-1615400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:1611200-1614000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:1611200-1614600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:1611200-1615600	Bivalent/Poised TSS	Left Ventricle	heart
18	chr6:1612000-1615400	Bivalent/Poised TSS	NH-A	brain
19	chr6:1612200-1613800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:1612200-1614000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:1612200-1614200	Bivalent/Poised TSS	Fetal Kidney	kidney
22	chr6:1612200-1614200	Weak transcription	Spleen	Spleen
23	chr6:1612200-1614200	Bivalent/Poised TSS	NHDF-Ad	bronchial
24	chr6:1612200-1615400	Bivalent/Poised TSS	Psoas Muscle	Psoas
25	chr6:1612200-1616200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:1612200-1617000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
27	chr6:1612400-1613800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:1612400-1613800	Bivalent/Poised TSS	Fetal Thymus	thymus
29	chr6:1612400-1614000	Active TSS	Pancreas	Pancrea
30	chr6:1612400-1614000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr6:1612400-1614200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
32	chr6:1612400-1614400	Weak transcription	Gastric	stomach
33	chr6:1612400-1614600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
34	chr6:1612400-1615000	Active TSS	Ovary	ovary
35	chr6:1612400-1615200	Active TSS	Right Ventricle	heart
36	chr6:1612600-1614400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr6:1612600-1614400	Bivalent/Poised TSS	Thymus	Thymus
38	chr6:1612600-1614800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:1612800-1614000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:1612800-1614000	Active TSS	Aorta	Aorta
41	chr6:1612800-1614200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr6:1612800-1616000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr6:1612800-1617000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
44	chr6:1613000-1613800	Weak transcription	HSMM	muscle
45	chr6:1613000-1615800	Active TSS	Osteobl	bone
46	chr6:1613000-1616000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:1613200-1613800	Bivalent Enhancer	Primary T cells from cord blood	blood
48	chr6:1613200-1614400	Active TSS	HSMMtube	muscle
49	chr6:1613400-1613800	Bivalent/Poised TSS	Placenta	Placenta
50	chr6:1613400-1613800	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links