Variant report

Variant	rs10146357
Chromosome Location	chr14:31103790-31103791
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	GATA3	chr14:31103750-31104265	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr14:31103781-31104421	MCF-7	breast:	n/a	n/a
3	GATA3	chr14:31103624-31104535	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:31095388..31097484-chr14:31101904..31104566,2	MCF-7	breast:
2	chr14:31101730..31104155-chr14:31107866..31110799,3	MCF-7	breast:

Variant related genes	Relation type
SCFD1	TF binding region
ENSG00000092108	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10130830	0.81[CHB][hapmap]
rs10131166	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10141944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10142331	0.81[CHB][hapmap]
rs10147257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10149966	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113946	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs11156637	0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1123860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11622076	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11623154	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11625381	0.81[CHB][hapmap]
rs11627421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11628700	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11846293	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11846408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11846420	0.85[CHD][hapmap]
rs11851205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12434151	0.81[CHB][hapmap]
rs12586678	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12882048	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12882931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12888568	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs12894186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs142983	0.82[CEU][hapmap]
rs17096941	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17097023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17097160	0.88[CEU][hapmap];0.91[MEX][hapmap]
rs172946	0.81[CHB][hapmap]
rs2038451	0.87[CEU][hapmap]
rs2057284	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2070339	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2070340	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs229144	0.81[CHB][hapmap]
rs229150	0.80[CHB][hapmap];0.85[CHD][hapmap]
rs229152	0.81[CHB][hapmap]
rs229154	0.81[CHB][hapmap]
rs229155	0.85[CHD][hapmap]
rs229161	0.81[CHB][hapmap]
rs229190	0.81[CHB][hapmap]
rs229209	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs229211	0.81[CHB][hapmap]
rs229244	0.86[CHB][hapmap];0.80[CHD][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs230340	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs230351	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs230364	0.81[CHB][hapmap]
rs230366	0.81[CHB][hapmap]
rs2378780	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs2378782	0.81[CHB][hapmap]
rs28567474	0.98[ASN][1000 genomes]
rs34935871	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35069045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35389182	0.82[EUR][1000 genomes]
rs3736773	0.88[CEU][hapmap]
rs4430662	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61976741	0.91[EUR][1000 genomes]
rs6571356	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6571357	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6571361	0.81[CHB][hapmap]
rs7141333	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7141624	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7144204	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs7147530	0.81[CHB][hapmap]
rs7149113	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153509	0.81[CHB][hapmap]
rs7154847	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs7493549	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs761956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs8006314	0.81[CHB][hapmap]
rs8008094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8012494	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs8013017	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8015536	1.00[CHB][hapmap]
rs8018993	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8019637	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322864	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs9806111	0.81[CHB][hapmap];0.85[CHD][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10146357	SCFD1	cis	cerebellum	SCAN
rs10146357	G2E3	cis	parietal	SCAN
rs10146357	SCFD1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31092200-31104000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:31092200-31121000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr14:31092200-31133200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr14:31092200-31133200	Weak transcription	Esophagus	oesophagus
5	chr14:31092400-31122800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:31092800-31113200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr14:31092800-31114200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:31093400-31103800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr14:31093400-31103800	Weak transcription	Brain Hippocampus Middle	brain
10	chr14:31093600-31103800	Weak transcription	Brain Germinal Matrix	brain
11	chr14:31093600-31103800	Weak transcription	Fetal Lung	lung
12	chr14:31093600-31107200	Weak transcription	Right Ventricle	heart
13	chr14:31093600-31127200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:31093800-31113800	Weak transcription	Brain Substantia Nigra	brain
15	chr14:31093800-31159600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr14:31094000-31111200	Weak transcription	HSMMtube	muscle
17	chr14:31094000-31113200	Weak transcription	Fetal Brain Male	brain
18	chr14:31094000-31122000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:31094200-31111200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:31094200-31121000	Weak transcription	Spleen	Spleen
21	chr14:31094200-31145200	Weak transcription	Small Intestine	intestine
22	chr14:31094600-31104600	Weak transcription	Colon Smooth Muscle	Colon
23	chr14:31094600-31109200	Weak transcription	K562	blood
24	chr14:31095200-31112400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:31095200-31119200	Weak transcription	Colonic Mucosa	Colon
26	chr14:31095600-31114400	Weak transcription	Fetal Heart	heart
27	chr14:31095800-31104000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr14:31095800-31110200	Weak transcription	Stomach Mucosa	stomach
29	chr14:31095800-31111000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr14:31095800-31121000	Weak transcription	Ovary	ovary
31	chr14:31095800-31121000	Weak transcription	Thymus	Thymus
32	chr14:31096000-31104000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr14:31096000-31111200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:31096000-31116600	Weak transcription	Lung	lung
35	chr14:31096000-31121000	Weak transcription	Pancreas	Pancrea
36	chr14:31096000-31167400	Weak transcription	Gastric	stomach
37	chr14:31096200-31113200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:31097200-31133800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr14:31097800-31104000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr14:31099400-31105400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr14:31099400-31106400	Strong transcription	Liver	Liver
42	chr14:31099400-31106800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr14:31099400-31107400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr14:31099400-31109400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr14:31099400-31110200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr14:31099600-31105000	Strong transcription	Placenta	Placenta
47	chr14:31099600-31105200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:31099600-31105200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:31099600-31105200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr14:31099600-31105200	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links