Variant report

Variant	rs34072166
Chromosome Location	chr14:35328325-35328326
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35327682..35333013-chr14:35342164..35345913,7	MCF-7	breast:
2	chr14:35326748..35329780-chr14:35341273..35343392,3	K562	blood:
3	chr14:35248368..35250493-chr14:35326583..35328999,2	K562	blood:
4	chr14:35328294..35330963-chr14:35340568..35342148,2	MCF-7	breast:
5	chr14:35326620..35331114-chr14:35341178..35344775,5	K562	blood:

Variant related genes	Relation type
ENSG00000198604	Chromatin interaction
ENSG00000258738	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10136352	0.81[JPT][hapmap]
rs10150083	0.83[JPT][hapmap]
rs11847610	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1200414	0.81[JPT][hapmap]
rs12431818	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12432567	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12433706	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs12435778	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12435859	0.87[AFR][1000 genomes]
rs12586459	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12586462	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12587021	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs12587251	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12587390	0.81[CHB][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12587913	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588318	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12590112	0.90[JPT][hapmap]
rs12590268	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1400745	0.90[JPT][hapmap]
rs17102726	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17102768	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17102795	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17102829	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs17526787	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs17526884	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs1959154	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2295468	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2383675	0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs2383676	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2383677	0.93[CHB][hapmap];0.95[JPT][hapmap]
rs34245772	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783315	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3783316	0.81[JPT][hapmap]
rs5016735	0.86[ASN][1000 genomes]
rs55979964	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs58268256	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58587072	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59678582	0.87[AFR][1000 genomes]
rs61981198	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61981200	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61981202	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61981204	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61981228	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61981232	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61981234	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61981236	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61981237	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61988010	0.89[ASN][1000 genomes]
rs61988011	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61988012	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61988013	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61988044	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988045	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7142012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148400	0.81[JPT][hapmap]
rs7150069	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7153289	0.95[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs7155348	0.84[ASN][1000 genomes]
rs8005470	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8005659	0.95[CEU][hapmap];0.81[CHB][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.91[YRI][hapmap]
rs8010504	0.85[ASN][1000 genomes]
rs8010579	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392700	chr14:34989406-35365530	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34072166	SNX6	cis	parietal	SCAN
rs34072166	SCFD1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35269400-35341600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr14:35272400-35333600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr14:35276200-35342400	Weak transcription	Pancreas	Pancrea
4	chr14:35276400-35329600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:35276400-35330000	Weak transcription	Colonic Mucosa	Colon
6	chr14:35307000-35333800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:35312200-35336200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:35312600-35328600	Weak transcription	Fetal Kidney	kidney
9	chr14:35312600-35335200	Weak transcription	Right Ventricle	heart
10	chr14:35312800-35330600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr14:35312800-35331600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:35312800-35336600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr14:35312800-35341400	Weak transcription	Colon Smooth Muscle	Colon
14	chr14:35312800-35341600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:35312800-35341600	Weak transcription	Psoas Muscle	Psoas
16	chr14:35312800-35342200	Weak transcription	Small Intestine	intestine
17	chr14:35312800-35342400	Weak transcription	Left Ventricle	heart
18	chr14:35313000-35330800	Weak transcription	Adipose Nuclei	Adipose
19	chr14:35313600-35341600	Weak transcription	Brain Germinal Matrix	brain
20	chr14:35318200-35331400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:35318400-35330000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:35318400-35342200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr14:35319200-35331600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:35320200-35332200	Strong transcription	HepG2	liver
25	chr14:35320400-35330400	Weak transcription	HMEC	breast
26	chr14:35320800-35329400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr14:35321600-35331400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:35321800-35342400	Weak transcription	Gastric	stomach
29	chr14:35322000-35331600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr14:35322200-35329200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:35322400-35330200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr14:35322600-35341400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr14:35322800-35330000	Strong transcription	Fetal Intestine Small	intestine
34	chr14:35322800-35330600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:35322800-35341200	Weak transcription	HSMMtube	muscle
36	chr14:35322800-35342200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr14:35323000-35330400	Weak transcription	Fetal Brain Female	brain
38	chr14:35323200-35341800	Weak transcription	NHLF	lung
39	chr14:35323400-35328400	Strong transcription	NHEK	skin
40	chr14:35323400-35329400	Weak transcription	Fetal Intestine Large	intestine
41	chr14:35323800-35342600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr14:35324200-35329000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:35324600-35329200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr14:35324600-35335200	Weak transcription	Lung	lung
45	chr14:35324600-35341600	Weak transcription	Fetal Lung	lung
46	chr14:35324600-35342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr14:35324800-35342200	Weak transcription	Ovary	ovary
48	chr14:35325000-35328600	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr14:35325200-35330200	Strong transcription	Fetal Muscle Leg	muscle
50	chr14:35325600-35331200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links