Variant report

Variant	rs229247
Chromosome Location	chr14:31057986-31057987
allele	C/T
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	STAT3	chr14:31057954-31057993	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31055576..31058014-chr14:31058559..31061042,2	MCF-7	breast:
2	chr14:31057134..31058920-chr14:31060095..31063812,3	MCF-7	breast:

Variant related genes	Relation type
G2E3	TF binding region
ENSG00000092140	Chromatin interaction

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

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

rs_ID	r²[population]
rs10130830	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10139154	0.82[EUR][1000 genomes]
rs10142331	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10147505	0.86[EUR][1000 genomes]
rs11625381	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11846420	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12434151	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs151123	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs170663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs170665	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs172946	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs179287	0.91[EUR][1000 genomes]
rs183467	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2045180	0.97[EUR][1000 genomes]
rs2070339	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229141	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs229143	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229144	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229145	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229150	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229152	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229154	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229155	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229156	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229161	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229162	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229171	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229173	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229176	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs229179	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229184	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs229190	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229194	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229195	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs229200	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229201	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229206	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229209	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229211	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs229221	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs229222	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229227	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs229228	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229231	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs229235	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229236	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229237	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229240	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229243	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs230351	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs230353	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs230356	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230360	0.80[EUR][1000 genomes]
rs230364	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs230366	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2378781	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2378782	0.83[EUR][1000 genomes]
rs34558066	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs448175	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4981767	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58049	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61976711	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7141161	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7142948	0.87[EUR][1000 genomes]
rs7144204	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7147530	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7152417	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7153509	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7153747	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7154847	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7158351	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9806111	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[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
rs229247	SCFD1	cis	Thyroid	GTEx
rs229247	SCFD1	cis	Whole Blood	GTEx

Chromatin state (count:115 , 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	chr14:31029400-31059400	Weak transcription	Left Ventricle	heart
4	chr14:31029400-31060400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr14:31030400-31059200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:31032000-31067400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr14:31032400-31067200	Weak transcription	Fetal Stomach	stomach
8	chr14:31033800-31070000	Weak transcription	Lung	lung
9	chr14:31034000-31059200	Weak transcription	Fetal Lung	lung
10	chr14:31040200-31069800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr14:31043000-31079600	Weak transcription	Gastric	stomach
12	chr14:31043000-31090600	Weak transcription	Small Intestine	intestine
13	chr14:31045000-31070000	Weak transcription	Aorta	Aorta
14	chr14:31045800-31067400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr14:31046800-31069800	Weak transcription	Fetal Kidney	kidney
16	chr14:31047000-31058800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr14:31047000-31058800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr14:31047000-31059000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr14:31047000-31059000	Weak transcription	NH-A	brain
20	chr14:31047000-31069800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:31047000-31079600	Weak transcription	Pancreas	Pancrea
22	chr14:31047200-31059000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr14:31047200-31063600	Weak transcription	Fetal Intestine Small	intestine
24	chr14:31048600-31060800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr14:31049000-31060400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr14:31049600-31079600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:31050200-31079800	Weak transcription	Brain Angular Gyrus	brain
28	chr14:31050400-31059000	Weak transcription	Placenta	Placenta
29	chr14:31050800-31067800	Weak transcription	Ovary	ovary
30	chr14:31051000-31059800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:31051000-31060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr14:31051800-31064600	Strong transcription	HSMM	muscle
33	chr14:31051800-31079600	Weak transcription	Fetal Brain Male	brain
34	chr14:31052000-31077400	Weak transcription	Psoas Muscle	Psoas
35	chr14:31052400-31060400	Weak transcription	NHLF	lung
36	chr14:31053600-31058600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr14:31053600-31079800	Weak transcription	Brain Substantia Nigra	brain
38	chr14:31053800-31059200	Weak transcription	Primary T cells from cord blood	blood
39	chr14:31053800-31059400	Weak transcription	Fetal Muscle Leg	muscle
40	chr14:31053800-31059800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr14:31053800-31067600	Weak transcription	Brain Anterior Caudate	brain
42	chr14:31053800-31070200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr14:31053800-31090600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr14:31054000-31058800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:31054000-31060400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr14:31054200-31090400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:31054400-31066800	Weak transcription	Brain Germinal Matrix	brain
48	chr14:31054600-31058200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr14:31054600-31058800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr14:31054600-31062800	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links