Variant report

Variant	rs61990686
Chromosome Location	chr14:78226339-78226340
allele	C/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	CTCF	chr14:78226258-78228556	A549	lung:	n/a	n/a
2	POLR2A	chr14:78225974-78228288	IMR90	lung:	n/a	n/a
3	POLR2A	chr14:78226289-78228060	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:78223413..78230716-chr14:78265065..78269735,15	MCF-7	breast:
2	chr14:78217096..78219959-chr14:78223868..78226613,3	K562	blood:
3	chr14:78003135..78004695-chr14:78224805..78226945,2	K562	blood:
4	chr14:78225549..78228360-chr14:78265163..78268062,4	K562	blood:

Variant related genes	Relation type
C14orf178	TF binding region
ENSG00000063761	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1030151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1030152	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17106259	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17106364	1.00[EUR][1000 genomes]
rs45519831	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45611739	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4899669	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4899671	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4899672	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4903628	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4903630	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4903633	0.89[EUR][1000 genomes]
rs57485881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57654091	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58390480	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60228583	0.94[EUR][1000 genomes]
rs61435552	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61990683	0.93[EUR][1000 genomes]
rs61990684	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61990688	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61990689	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61990690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61990695	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61990716	1.00[EUR][1000 genomes]
rs61990717	1.00[EUR][1000 genomes]
rs61990718	1.00[EUR][1000 genomes]
rs61990719	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61990721	0.97[EUR][1000 genomes]
rs61990722	0.97[EUR][1000 genomes]
rs61992865	0.80[EUR][1000 genomes]
rs61992869	0.80[EUR][1000 genomes]
rs61992870	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61992912	0.83[EUR][1000 genomes]
rs61992917	0.83[EUR][1000 genomes]
rs61992919	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61992921	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61993669	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61993672	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6574390	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7143265	0.83[EUR][1000 genomes]
rs7143382	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7146446	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7147748	0.83[EUR][1000 genomes]
rs7152638	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7156186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7156905	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7160307	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8007598	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8014720	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8019064	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv2754594	chr14:78222798-78275549	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61990686	RPL21P10	cis	Muscle Skeletal	GTEx
rs61990686	RPL21P10	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78201600-78226600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78214200-78226600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:78217000-78226600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:78218000-78226400	Weak transcription	Aorta	Aorta
5	chr14:78218200-78226400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:78218400-78226400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr14:78219800-78226400	Weak transcription	HSMM	muscle
8	chr14:78221400-78226400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:78221600-78226400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr14:78221600-78226600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:78223000-78226600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr14:78223200-78226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:78223600-78226400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr14:78223600-78226400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr14:78223600-78226400	Enhancers	Adipose Nuclei	Adipose
16	chr14:78223800-78226400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:78224200-78226400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:78224600-78226400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr14:78224600-78226400	Enhancers	Psoas Muscle	Psoas
20	chr14:78224800-78226400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:78224800-78226400	Enhancers	Liver	Liver
22	chr14:78224800-78226400	Enhancers	Brain Substantia Nigra	brain
23	chr14:78224800-78226400	Genic enhancers	Fetal Stomach	stomach
24	chr14:78224800-78226400	Enhancers	Pancreas	Pancrea
25	chr14:78225000-78226400	Enhancers	Brain Anterior Caudate	brain
26	chr14:78225000-78226400	Enhancers	Fetal Heart	heart
27	chr14:78225000-78226400	Enhancers	Right Atrium	heart
28	chr14:78225200-78226400	Enhancers	Brain Cingulate Gyrus	brain
29	chr14:78225200-78226400	Enhancers	Fetal Brain Male	brain
30	chr14:78225200-78226400	Enhancers	Gastric	stomach
31	chr14:78225200-78226400	Enhancers	Lung	lung
32	chr14:78225200-78226400	Enhancers	Ovary	ovary
33	chr14:78225200-78226400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr14:78225200-78226400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr14:78225200-78226400	Genic enhancers	Thymus	Thymus
36	chr14:78225200-78226600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr14:78225200-78226600	Enhancers	Left Ventricle	heart
38	chr14:78225400-78226400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr14:78225400-78226400	Enhancers	Primary hematopoietic stem cells	blood
40	chr14:78225400-78226400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr14:78225400-78226400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr14:78225400-78226400	Weak transcription	HSMMtube	muscle
43	chr14:78225400-78226600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr14:78225400-78226600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr14:78225600-78226400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr14:78225600-78226400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr14:78225600-78226400	Enhancers	Brain Angular Gyrus	brain
48	chr14:78225600-78226400	Enhancers	Colon Smooth Muscle	Colon
49	chr14:78225600-78226400	Weak transcription	Fetal Kidney	kidney
50	chr14:78225600-78226400	Enhancers	Stomach Mucosa	stomach

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