Variant report

Variant	rs10142331
Chromosome Location	chr14:31197026-31197027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31189606..31191411-chr14:31195229..31197325,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10130830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10139154	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10146357	0.81[CHB][hapmap]
rs10147257	0.82[CHB][hapmap]
rs10147505	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1123860	0.82[CHB][hapmap]
rs11625381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11627421	0.81[CHB][hapmap]
rs11628700	0.81[CHB][hapmap]
rs11846408	0.81[CHB][hapmap]
rs11846420	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12432098	1.00[YRI][hapmap]
rs12434151	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12882931	0.81[CHB][hapmap]
rs151123	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs170663	0.83[EUR][1000 genomes]
rs170665	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17097023	0.80[CHB][hapmap]
rs172946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs179287	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1950882	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2070339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070340	0.81[CHB][hapmap]
rs2273521	0.82[CHB][hapmap]
rs2273522	0.80[CHB][hapmap]
rs229141	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229143	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs229144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229145	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs229150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229155	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229156	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs229161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229162	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229173	0.81[EUR][1000 genomes]
rs229176	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs229179	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs229184	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs229190	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs229194	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs229195	0.83[EUR][1000 genomes]
rs229200	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs229201	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs229206	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs229207	0.86[ASN][1000 genomes]
rs229209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs229211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs229231	0.85[EUR][1000 genomes]
rs229235	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs229236	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs229237	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs229240	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs229243	0.84[EUR][1000 genomes]
rs229247	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs230340	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs230343	0.86[ASN][1000 genomes]
rs230351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230353	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230356	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230360	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs230364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2378780	0.81[CHB][hapmap]
rs2378781	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34558066	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35069045	0.81[CHB][hapmap]
rs4430662	0.81[CHB][hapmap]
rs448175	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4981767	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4981770	0.84[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs58049	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61976711	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6571361	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7141161	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7141333	0.82[CHB][hapmap]
rs7142948	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7144204	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7147530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152417	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7153509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7153747	0.91[CEU][hapmap]
rs7154847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7158351	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761956	0.82[CHB][hapmap]
rs8006314	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs8008094	0.81[CHB][hapmap]
rs8012494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8013017	0.82[CHB][hapmap]
rs8015536	0.82[CHB][hapmap]
rs9322864	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs9806111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10142331	SCFD1	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31113800-31205400	Weak transcription	Fetal Brain Male	brain
2	chr14:31122800-31205200	Weak transcription	Brain Angular Gyrus	brain
3	chr14:31123000-31212000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr14:31123400-31216400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr14:31133800-31197400	Weak transcription	Aorta	Aorta
6	chr14:31153600-31198800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:31160000-31206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr14:31160000-31207200	Weak transcription	Right Ventricle	heart
9	chr14:31160400-31205000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:31160800-31197400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr14:31160800-31198600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:31160800-31206200	Weak transcription	Small Intestine	intestine
13	chr14:31161800-31199000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr14:31162200-31199200	Strong transcription	HepG2	liver
15	chr14:31162400-31204000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:31165000-31208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:31166000-31204200	Weak transcription	Colonic Mucosa	Colon
18	chr14:31166000-31205600	Weak transcription	Thymus	Thymus
19	chr14:31166400-31214200	Weak transcription	Pancreas	Pancrea
20	chr14:31168200-31205800	Weak transcription	Esophagus	oesophagus
21	chr14:31168200-31206000	Weak transcription	Gastric	stomach
22	chr14:31168200-31208600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:31171600-31205800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr14:31173600-31199200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr14:31177600-31205400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr14:31179000-31207400	Weak transcription	Fetal Kidney	kidney
27	chr14:31179200-31205200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr14:31179400-31197400	Weak transcription	Dnd41	blood
29	chr14:31180000-31205400	Weak transcription	NHLF	lung
30	chr14:31180800-31199000	Weak transcription	Fetal Intestine Small	intestine
31	chr14:31181600-31207000	Weak transcription	Hela-S3	cervix
32	chr14:31183800-31199000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr14:31184000-31199400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:31184400-31199000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr14:31185000-31199000	Strong transcription	Liver	Liver
36	chr14:31186000-31204000	Weak transcription	Brain Anterior Caudate	brain
37	chr14:31186400-31206200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:31190800-31197400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:31191000-31199400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:31191600-31199400	Strong transcription	Adipose Nuclei	Adipose
41	chr14:31192200-31198200	Strong transcription	Primary T cells from cord blood	blood
42	chr14:31192200-31199400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr14:31192200-31199400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr14:31192400-31197600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr14:31192800-31204200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr14:31193000-31207200	Weak transcription	Brain Germinal Matrix	brain
47	chr14:31193000-31207800	Weak transcription	A549	lung
48	chr14:31193400-31199400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr14:31193600-31199400	Strong transcription	Primary B cells from cord blood	blood
50	chr14:31194200-31197800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links