Variant report

Variant	rs55905614
Chromosome Location	chr6:1709367-1709368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1702313..1705686-chr6:1707242..1710657,4	K562	blood:
2	chr6:1706527..1710172-chr6:1711910..1715681,3	K562	blood:
3	chr6:1602365..1603969-chr6:1707557..1710103,2	MCF-7	breast:
4	chr6:1708677..1711111-chr6:1726818..1728968,2	K562	blood:
5	chr6:1708672..1711562-chr6:1713048..1715527,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1022547	0.97[EUR][1000 genomes]
rs1022549	0.94[EUR][1000 genomes]
rs1022550	0.94[EUR][1000 genomes]
rs17134216	0.96[EUR][1000 genomes]
rs1963147	0.87[EUR][1000 genomes]
rs4129868	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4499972	0.98[EUR][1000 genomes]
rs4959596	0.94[EUR][1000 genomes]
rs58177268	0.98[EUR][1000 genomes]
rs62388327	0.97[EUR][1000 genomes]
rs62388328	0.97[EUR][1000 genomes]
rs62388329	0.95[EUR][1000 genomes]
rs62388331	0.98[EUR][1000 genomes]
rs67143983	0.98[EUR][1000 genomes]
rs73405529	0.97[EUR][1000 genomes]
rs7742462	0.93[EUR][1000 genomes]
rs7746883	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
5	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
6	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
7	nsv1015682	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv538092	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv432843	chr6:1694719-1725261	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1814339	chr6:1702106-1716710	Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55905614	FOXC1	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1679600-1715600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1690000-1715000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1693600-1718200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:1694000-1709400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
8	chr6:1699800-1716600	Weak transcription	Primary T cells from cord blood	blood
9	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
10	chr6:1703600-1720800	Weak transcription	Right Atrium	heart
11	chr6:1704000-1721000	Weak transcription	Lung	lung
12	chr6:1704200-1715600	Weak transcription	Esophagus	oesophagus
13	chr6:1704200-1725200	Weak transcription	Primary B cells from cord blood	blood
14	chr6:1704600-1720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:1704800-1714800	Weak transcription	Aorta	Aorta
16	chr6:1705600-1709600	Strong transcription	HepG2	liver
17	chr6:1705800-1724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:1706000-1724200	Weak transcription	NHEK	skin
19	chr6:1706800-1726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:1707200-1709400	Weak transcription	Gastric	stomach
21	chr6:1707200-1724600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:1707600-1712800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:1707800-1724600	Weak transcription	GM12878-XiMat	blood
24	chr6:1708000-1709400	Enhancers	Fetal Kidney	kidney
25	chr6:1708200-1724600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:1708400-1710200	Strong transcription	Fetal Intestine Small	intestine
27	chr6:1708600-1710200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:1708800-1709400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:1708800-1709600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:1708800-1717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:1709000-1710800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:1709200-1709600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:1709200-1709800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:1709200-1709800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr6:1709200-1709800	Enhancers	Spleen	Spleen
36	chr6:1709200-1710000	Enhancers	Pancreas	Pancrea
37	chr6:1709200-1710000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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