Variant report

Variant	rs10450908
Chromosome Location	chr14:21977497-21977498
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:21977411-21977562	ProgFib	skin:	n/a	n/a
2	POLR2A	chr14:21977113-21977870	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:21976926..21983845-chr14:21991695..21998209,25	K562	blood:
2	chr14:21943182..21946742-chr14:21976824..21981257,10	MCF-7	breast:
3	chr14:21924214..21926252-chr14:21977009..21978995,2	K562	blood:
4	chr14:21977163..21984004-chr14:21985497..21991656,11	K562	blood:
5	chr14:21921735..21926252-chr14:21977495..21980798,4	K562	blood:
6	chr14:21943174..21947446-chr14:21976603..21980796,8	K562	blood:

No data

Variant related genes	Relation type
METTL3	TF binding region
ENSG00000165821	Chromatin interaction
ENSG00000100888	Chromatin interaction
ENSG00000092203	Chromatin interaction
ENSG00000257096	Chromatin interaction
ENSG00000129472	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10450907	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061027	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11850178	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852218	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13329035	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17516362	0.89[EUR][1000 genomes]
rs17792712	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes]
rs2282046	0.81[JPT][hapmap]
rs3168880	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3762163	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4417466	0.83[CHB][hapmap]
rs55690316	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58901398	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61973218	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61973219	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61973220	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61973223	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66771279	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs719785	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10450908	C14orf92	cis	multi-tissue	Pritchard
rs10450908	TOX4	Cis_1M	lymphoblastoid	RTeQTL
rs10450908	METTL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21946200-21977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:21947000-21978000	Weak transcription	Fetal Heart	heart
3	chr14:21964000-21977800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:21967800-21978600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:21971800-21978000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr14:21971800-21978000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr14:21971800-21978200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:21971800-21978200	Weak transcription	Stomach Mucosa	stomach
9	chr14:21972000-21977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:21972000-21977600	Weak transcription	Brain Angular Gyrus	brain
11	chr14:21972000-21977600	Weak transcription	Brain Substantia Nigra	brain
12	chr14:21972000-21977600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr14:21972000-21978000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr14:21972000-21978000	Weak transcription	NHDF-Ad	bronchial
15	chr14:21972000-21978200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:21972000-21978200	Weak transcription	Fetal Kidney	kidney
17	chr14:21972000-21978200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:21972000-21978200	Weak transcription	Right Ventricle	heart
19	chr14:21972000-21978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:21972000-21978600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:21972000-21978600	Weak transcription	Aorta	Aorta
22	chr14:21972000-21978600	Weak transcription	Esophagus	oesophagus
23	chr14:21972000-21978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:21972200-21978200	Weak transcription	Colonic Mucosa	Colon
25	chr14:21972600-21977600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr14:21973400-21977600	Weak transcription	HUVEC	blood vessel
27	chr14:21974200-21977600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr14:21974600-21977600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr14:21974600-21977600	Strong transcription	Fetal Stomach	stomach
30	chr14:21974800-21977600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:21974800-21977600	Strong transcription	A549	lung
32	chr14:21974800-21977800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr14:21975200-21977600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr14:21975600-21977600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:21975600-21977600	Strong transcription	Placenta	Placenta
36	chr14:21975600-21977600	Genic enhancers	Dnd41	blood
37	chr14:21975800-21977600	Genic enhancers	HepG2	liver
38	chr14:21975800-21977800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr14:21976000-21977600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:21976000-21977800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr14:21976000-21978000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr14:21976200-21977600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr14:21976200-21977800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:21976400-21977600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr14:21976400-21977600	Weak transcription	Fetal Brain Female	brain
46	chr14:21976400-21977800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr14:21976400-21978000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:21976400-21978000	Weak transcription	HSMMtube	muscle
49	chr14:21976400-21978200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr14:21976400-21978200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links