Variant report

Variant	rs229194
Chromosome Location	chr14:31045181-31045182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10130830	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10139154	0.82[EUR][1000 genomes]
rs10142331	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10147505	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11625381	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11846420	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12434151	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs151123	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs170663	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs170665	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs172946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs179287	0.90[EUR][1000 genomes]
rs183467	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2045180	0.95[EUR][1000 genomes]
rs2070339	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs229141	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229143	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229144	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229145	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229150	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229152	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229154	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229155	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229156	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229161	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229162	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229171	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229173	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229176	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs229179	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229184	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229190	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs229195	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229206	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229209	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229211	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229221	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229222	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229227	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229228	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229231	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229235	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229236	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229237	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229240	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229243	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229247	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs230351	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230353	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230356	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230360	0.81[EUR][1000 genomes]
rs230364	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230366	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2378781	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2378782	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34558066	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448175	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4981767	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61976711	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7141161	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7142948	0.85[EUR][1000 genomes]
rs7144204	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7147530	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7152417	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7153509	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7153747	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7154847	0.90[EUR][1000 genomes]
rs7158351	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9806111	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229194	SCFD1	cis	Thyroid	GTEx
rs229194	SCFD1	cis	Whole Blood	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31029000-31071800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:31029200-31071800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:31029400-31059400	Weak transcription	Left Ventricle	heart
4	chr14:31029400-31060400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr14:31029800-31054000	Weak transcription	Fetal Intestine Large	intestine
6	chr14:31030200-31053200	Weak transcription	Fetal Muscle Leg	muscle
7	chr14:31030400-31046600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:31030400-31050600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:31030400-31050600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr14:31030400-31056600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr14:31030400-31059200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:31030600-31046600	Weak transcription	NH-A	brain
13	chr14:31030800-31046600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr14:31031000-31052000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:31032000-31067400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr14:31032200-31046600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr14:31032200-31056400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:31032400-31049400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr14:31032400-31067200	Weak transcription	Fetal Stomach	stomach
20	chr14:31032600-31051600	Weak transcription	Fetal Thymus	thymus
21	chr14:31032600-31051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:31032800-31051600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:31032800-31053200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr14:31033600-31046600	Weak transcription	Thymus	Thymus
25	chr14:31033800-31046600	Weak transcription	Fetal Intestine Small	intestine
26	chr14:31033800-31070000	Weak transcription	Lung	lung
27	chr14:31034000-31059200	Weak transcription	Fetal Lung	lung
28	chr14:31034400-31051800	Weak transcription	HSMM	muscle
29	chr14:31035200-31045400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr14:31035600-31054400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:31039400-31053200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:31039800-31050600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:31040000-31051600	Weak transcription	Dnd41	blood
34	chr14:31040200-31046600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:31040200-31046600	Weak transcription	Primary T cells from cord blood	blood
36	chr14:31040200-31069800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr14:31040600-31049600	Weak transcription	Osteobl	bone
38	chr14:31040600-31057400	Weak transcription	Hela-S3	cervix
39	chr14:31040800-31046600	Weak transcription	NHDF-Ad	bronchial
40	chr14:31041000-31046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr14:31041200-31051600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:31041600-31046600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:31041600-31046600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr14:31041600-31053200	Weak transcription	Brain Substantia Nigra	brain
45	chr14:31041800-31046600	Weak transcription	HepG2	liver
46	chr14:31041800-31046800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr14:31042200-31050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:31042400-31056600	Weak transcription	NHEK	skin
49	chr14:31042800-31050000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr14:31042800-31051000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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