Variant report

Variant	rs230360
Chromosome Location	chr14:31137375-31137376
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10130830	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10139154	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10142331	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10147505	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11625381	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11846420	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs151123	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs170663	0.83[EUR][1000 genomes]
rs170665	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs172946	0.83[EUR][1000 genomes]
rs179287	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2045180	0.83[EUR][1000 genomes]
rs2070339	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs229141	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs229143	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs229144	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229145	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229150	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229152	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229154	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229155	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229156	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229161	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229162	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229184	0.80[AMR][1000 genomes]
rs229194	0.81[EUR][1000 genomes]
rs229195	0.83[EUR][1000 genomes]
rs229200	0.82[EUR][1000 genomes]
rs229201	0.82[EUR][1000 genomes]
rs229206	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229207	0.82[AMR][1000 genomes]
rs229209	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229211	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229231	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs229235	0.83[AMR][1000 genomes]
rs229236	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs229237	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs229240	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs229243	0.82[EUR][1000 genomes]
rs229247	0.80[EUR][1000 genomes]
rs230340	0.85[AMR][1000 genomes]
rs230343	0.85[AMR][1000 genomes]
rs230351	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230353	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230356	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230364	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230366	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2378781	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2378782	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34558066	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs448175	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4981767	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58049	0.82[EUR][1000 genomes]
rs61976711	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7141161	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7142948	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7144204	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7147530	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7152417	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7153509	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7158351	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8012494	0.81[AMR][1000 genomes]
rs9806111	0.86[AMR][1000 genomes];0.86[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs230360	SCFD1	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31093800-31159600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:31094200-31145200	Weak transcription	Small Intestine	intestine
3	chr14:31096000-31167400	Weak transcription	Gastric	stomach
4	chr14:31110600-31141800	Weak transcription	Stomach Mucosa	stomach
5	chr14:31113800-31205400	Weak transcription	Fetal Brain Male	brain
6	chr14:31115000-31167600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr14:31115200-31138600	Weak transcription	Fetal Heart	heart
8	chr14:31115200-31159600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:31119000-31153200	Weak transcription	Right Ventricle	heart
10	chr14:31121600-31159600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr14:31122400-31159600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr14:31122600-31141400	Weak transcription	Psoas Muscle	Psoas
13	chr14:31122600-31152200	Weak transcription	Spleen	Spleen
14	chr14:31122800-31205200	Weak transcription	Brain Angular Gyrus	brain
15	chr14:31123000-31212000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr14:31123400-31216400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr14:31123600-31159800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr14:31123600-31165400	Weak transcription	Colonic Mucosa	Colon
19	chr14:31124400-31148200	Weak transcription	Brain Substantia Nigra	brain
20	chr14:31124400-31152600	Weak transcription	Brain Hippocampus Middle	brain
21	chr14:31124400-31160200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr14:31124400-31171400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr14:31125000-31159600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr14:31125200-31152400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:31125200-31170000	Weak transcription	Colon Smooth Muscle	Colon
26	chr14:31125400-31152400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr14:31125400-31160000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr14:31126000-31139800	Weak transcription	K562	blood
29	chr14:31126200-31151800	Weak transcription	NHLF	lung
30	chr14:31126400-31142800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr14:31126400-31151200	Weak transcription	HMEC	breast
32	chr14:31128200-31142400	Weak transcription	HUVEC	blood vessel
33	chr14:31128200-31144800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr14:31128200-31152200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:31128200-31152400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr14:31128200-31164600	Weak transcription	Brain Anterior Caudate	brain
37	chr14:31128200-31165600	Weak transcription	HSMMtube	muscle
38	chr14:31130800-31142800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr14:31130800-31142800	Weak transcription	Fetal Thymus	thymus
40	chr14:31131600-31139800	Weak transcription	NH-A	brain
41	chr14:31131600-31151200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr14:31131800-31139800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr14:31131800-31144200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:31132000-31139800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr14:31132200-31148800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr14:31132400-31160400	Weak transcription	Hela-S3	cervix
47	chr14:31133000-31140800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:31133000-31143000	Weak transcription	Placenta	Placenta
49	chr14:31133200-31139200	Weak transcription	Primary B cells from cord blood	blood
50	chr14:31133200-31160600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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