Variant report

Variant	rs170665
Chromosome Location	chr14:31068345-31068346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31067708..31069634-chr14:31090291..31092583,3	MCF-7	breast:
2	chr14:31067916..31070610-chr14:31073012..31074923,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10130830	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10139154	0.83[EUR][1000 genomes]
rs10142331	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10147505	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11625381	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11846420	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12434151	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs151123	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs170663	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs172946	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs179287	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs183467	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1950882	0.81[EUR][1000 genomes]
rs2045180	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2070339	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229141	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229143	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229144	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229145	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229150	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs229152	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229154	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229155	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229156	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229161	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229162	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229171	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229173	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229176	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229179	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229184	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229190	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229194	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229195	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229200	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229201	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229206	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229209	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229211	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229221	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229222	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229227	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229228	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229231	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs229235	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229236	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229237	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229240	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229243	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229244	0.82[EUR][1000 genomes]
rs229247	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230351	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs230353	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs230356	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs230360	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs230364	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs230366	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2378781	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2378782	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34558066	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448175	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981767	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58049	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61976711	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6571361	0.81[EUR][1000 genomes]
rs7141161	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7142948	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7144204	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7147530	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7152417	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7153509	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7153747	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7154847	0.91[EUR][1000 genomes]
rs7158351	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9806111	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs170665	SCFD1	cis	Whole Blood	GTEx
rs170665	SCFD1	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

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	chr14:31033800-31070000	Weak transcription	Lung	lung
4	chr14:31040200-31069800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:31043000-31079600	Weak transcription	Gastric	stomach
6	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
7	chr14:31045000-31070000	Weak transcription	Aorta	Aorta
8	chr14:31046800-31069800	Weak transcription	Fetal Kidney	kidney
9	chr14:31047000-31069800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:31047000-31079600	Weak transcription	Pancreas	Pancrea
11	chr14:31049600-31079600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:31050200-31079800	Weak transcription	Brain Angular Gyrus	brain
13	chr14:31051800-31079600	Weak transcription	Fetal Brain Male	brain
14	chr14:31052000-31077400	Weak transcription	Psoas Muscle	Psoas
15	chr14:31053600-31079800	Weak transcription	Brain Substantia Nigra	brain
16	chr14:31053800-31070200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr14:31054200-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:31054800-31072000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:31054800-31087200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:31055000-31086800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:31055400-31069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:31055400-31070000	Weak transcription	Colonic Mucosa	Colon
24	chr14:31055600-31088000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:31057200-31071800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:31057400-31077600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr14:31057800-31079800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr14:31058400-31080000	Weak transcription	Fetal Heart	heart
29	chr14:31058800-31069800	Weak transcription	Spleen	Spleen
30	chr14:31058800-31074800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr14:31059200-31069400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr14:31059600-31069200	Weak transcription	NHEK	skin
33	chr14:31059600-31069400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:31059800-31069400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr14:31059800-31080000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:31060000-31070000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr14:31061000-31069400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr14:31061000-31071800	Weak transcription	NHLF	lung
39	chr14:31061400-31070200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr14:31061600-31090400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr14:31062200-31069000	Weak transcription	Fetal Lung	lung
42	chr14:31063000-31069600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr14:31064200-31078200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:31064400-31087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:31064600-31073800	Strong transcription	Primary B cells from cord blood	blood
46	chr14:31064800-31078000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr14:31064800-31086600	Strong transcription	Dnd41	blood
48	chr14:31064800-31087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:31065000-31068400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr14:31065000-31075000	Strong transcription	Primary T cells fromperipheralblood	blood

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