Variant report

Variant	rs229162
Chromosome Location	chr14:31107564-31107565
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10130830	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10139154	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10142331	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10147505	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11625381	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11846420	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12434151	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs151123	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs170663	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs170665	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs172946	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs179287	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183467	0.84[EUR][1000 genomes]
rs1950882	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2045180	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070339	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229141	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229143	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs229144	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229145	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229150	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229152	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229155	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229171	0.84[EUR][1000 genomes]
rs229173	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229176	0.86[EUR][1000 genomes]
rs229179	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229184	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229190	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs229194	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229195	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229200	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229201	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229207	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs229209	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229211	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229221	0.83[EUR][1000 genomes]
rs229222	0.81[EUR][1000 genomes]
rs229227	0.84[EUR][1000 genomes]
rs229228	0.83[EUR][1000 genomes]
rs229231	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229235	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229236	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229237	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229240	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229243	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229247	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230340	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs230343	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs230351	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230353	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230356	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230360	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230364	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230366	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2378781	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2378782	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34558066	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35349033	0.85[ASN][1000 genomes]
rs448175	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4981767	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58049	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61976711	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6571361	0.87[EUR][1000 genomes]
rs7141161	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7142948	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7144204	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7147530	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152417	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7153509	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7154847	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7158351	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8012494	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9806111	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][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	nsv564169	chr14:30819087-31541494	Strong transcription Genic enhancers ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1036419	chr14:30969616-31224226	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv901581	chr14:30978745-31585289	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv564171	chr14:31068090-31149630	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229162	SCFD1	cis	Whole Blood	GTEx
rs229162	SCFD1	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31092200-31121000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:31092200-31133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:31092200-31133200	Weak transcription	Esophagus	oesophagus
4	chr14:31092400-31122800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:31092800-31113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:31092800-31114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:31093600-31127200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:31093800-31113800	Weak transcription	Brain Substantia Nigra	brain
9	chr14:31093800-31159600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:31094000-31111200	Weak transcription	HSMMtube	muscle
11	chr14:31094000-31113200	Weak transcription	Fetal Brain Male	brain
12	chr14:31094000-31122000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:31094200-31111200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:31094200-31121000	Weak transcription	Spleen	Spleen
15	chr14:31094200-31145200	Weak transcription	Small Intestine	intestine
16	chr14:31094600-31109200	Weak transcription	K562	blood
17	chr14:31095200-31112400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr14:31095200-31119200	Weak transcription	Colonic Mucosa	Colon
19	chr14:31095600-31114400	Weak transcription	Fetal Heart	heart
20	chr14:31095800-31110200	Weak transcription	Stomach Mucosa	stomach
21	chr14:31095800-31111000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr14:31095800-31121000	Weak transcription	Ovary	ovary
23	chr14:31095800-31121000	Weak transcription	Thymus	Thymus
24	chr14:31096000-31111200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:31096000-31116600	Weak transcription	Lung	lung
26	chr14:31096000-31121000	Weak transcription	Pancreas	Pancrea
27	chr14:31096000-31167400	Weak transcription	Gastric	stomach
28	chr14:31096200-31113200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr14:31097200-31133800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr14:31099400-31109400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr14:31099400-31110200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:31099600-31111000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr14:31099600-31113000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:31099600-31113200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr14:31099600-31113200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr14:31099600-31113600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr14:31099600-31113600	Strong transcription	HSMM	muscle
38	chr14:31099600-31114200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:31099600-31114400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:31099600-31133800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr14:31099600-31134000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:31100000-31109600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr14:31100000-31113000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr14:31100400-31108000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr14:31100600-31123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr14:31101200-31111600	Weak transcription	Fetal Intestine Small	intestine
47	chr14:31101200-31112200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr14:31101400-31111200	Weak transcription	Fetal Stomach	stomach
49	chr14:31101800-31111200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr14:31102000-31123600	Strong transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links