Variant report

Variant	rs2025342
Chromosome Location	chr6:1904885-1904886
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-9	chr6:1904213-1905355	NONHSAT106552
2	lnc-FOXC1-9	chr6:1903452-1905355	NONHSAT106553
3	lnc-FOXC1-9	chr6:1904182-1906085	NONHSAT106555

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs3778543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3800120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3800124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3895318	1.00[ASN][1000 genomes]
rs6596859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9405153	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9503044	1.00[AMR][1000 genomes]
rs9503046	1.00[AMR][1000 genomes]
rs9654658	1.00[AMR][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	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
2	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
3	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
4	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
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1851400-1909600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr6:1877600-1915200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:1890600-1911400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:1891800-1914800	Weak transcription	Colonic Mucosa	Colon
5	chr6:1895800-1910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:1895800-1911200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:1896000-1916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:1896400-1910800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:1896600-1905000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:1897200-1916200	Weak transcription	Thymus	Thymus
11	chr6:1897400-1915000	Weak transcription	Esophagus	oesophagus
12	chr6:1897400-1915000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:1898200-1905000	Weak transcription	HepG2	liver
14	chr6:1898600-1914800	Weak transcription	Gastric	stomach
15	chr6:1901600-1923400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:1902200-1910800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:1902400-1910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:1903400-1905200	Enhancers	Fetal Kidney	kidney
19	chr6:1903600-1905000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:1903600-1905600	Enhancers	Fetal Stomach	stomach
21	chr6:1903800-1905000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:1903800-1905000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:1903800-1905000	Enhancers	Adipose Nuclei	Adipose
24	chr6:1903800-1905200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr6:1903800-1905200	Enhancers	HUVEC	blood vessel
26	chr6:1903800-1905400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr6:1903800-1905400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:1904000-1905000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:1904000-1905000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:1904000-1905000	Enhancers	Aorta	Aorta
31	chr6:1904000-1905000	Enhancers	Fetal Muscle Leg	muscle
32	chr6:1904000-1905200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:1904000-1905200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:1904000-1905200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:1904000-1905200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:1904000-1905200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:1904000-1905200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:1904000-1905200	Enhancers	Fetal Muscle Trunk	muscle
39	chr6:1904000-1905200	Enhancers	Left Ventricle	heart
40	chr6:1904000-1905200	Enhancers	Right Atrium	heart
41	chr6:1904000-1905400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:1904000-1905400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr6:1904000-1905400	Enhancers	Pancreas	Pancrea
44	chr6:1904000-1913000	Weak transcription	Dnd41	blood
45	chr6:1904200-1905000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:1904200-1905200	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:1904200-1910800	Weak transcription	Psoas Muscle	Psoas
48	chr6:1904400-1905000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:1904400-1905000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:1904400-1912200	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links