Variant report

Variant	rs34852276
Chromosome Location	chr14:65428165-65428166
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	TCF12	chr14:65427254-65428183	MCF-7	breast:	n/a	chr14:65427681-65427691
2	MAX	chr14:65426488-65428322	MCF-7	breast:	n/a	chr14:65426954-65426963 chr14:65427960-65427976 chr14:65427936-65427946
3	RAD21	chr14:65427353-65428185	MCF-7	breast:	n/a	n/a
4	EP300	chr14:65427491-65428171	MCF-7	breast:	n/a	chr14:65427569-65427578
5	GATA3	chr14:65427094-65428342	MCF-7	breast:	n/a	chr14:65428194-65428201
6	MAX	chr14:65427377-65428284	MCF-7	breast:	n/a	chr14:65427960-65427976 chr14:65427936-65427946
7	HDAC2	chr14:65427351-65428438	MCF-7	breast:	n/a	n/a
8	MAX	chr14:65427492-65428168	ECC-1	luminal epithelium:	n/a	chr14:65427960-65427976 chr14:65427936-65427946
9	ELF1	chr14:65427433-65428356	MCF-7	breast:	n/a	chr14:65427567-65427578
10	NR2F2	chr14:65427399-65428384	MCF-7	breast:	n/a	n/a
11	GATA3	chr14:65427211-65428347	MCF-7	breast:	n/a	chr14:65428194-65428201
12	SIN3AK20	chr14:65427332-65428299	MCF-7	breast:	n/a	n/a
13	MXI1	chr14:65427177-65428574	SK-N-SH	brain:	n/a	n/a
14	NR2F2	chr14:65427323-65428521	MCF-7	breast:	n/a	n/a
15	GATA3	chr14:65427473-65428180	MCF-7	breast:	n/a	n/a
16	FOXM1	chr14:65427404-65428242	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:65409296..65411152-chr14:65426645..65429491,2	MCF-7	breast:
2	chr14:65381132..65383613-chr14:65427775..65429554,2	MCF-7	breast:
3	chr14:65427868..65430496-chr14:65442543..65444279,2	MCF-7	breast:
4	chr14:65428039..65432050-chr14:65432116..65435145,5	MCF-7	breast:
5	chr14:65426546..65429390-chr14:65452046..65455184,4	MCF-7	breast:
6	chr14:65426410..65429284-chr14:65447447..65450019,2	MCF-7	breast:

Variant related genes	Relation type
RAB15	TF binding region
ENSG00000176153	Chromatin interaction
ENSG00000257365	Chromatin interaction
ENSG00000258289	Chromatin interaction
ENSG00000125954	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11540873	0.82[AMR][1000 genomes]
rs11623886	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2277501	1.00[CEU][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2296325	0.88[ASN][1000 genomes]
rs2296326	1.00[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412105	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412106	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412107	0.86[ASW][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap]
rs3087955	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3759681	0.83[AMR][1000 genomes]
rs45454295	0.86[AMR][1000 genomes]
rs4899155	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4899158	0.96[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902352	0.87[CEU][hapmap]
rs6573586	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7143541	0.83[JPT][hapmap]
rs7359095	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8004904	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8007405	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8009893	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8010391	0.87[ASN][1000 genomes]
rs8016174	0.80[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33119	chr14:65421491-65434429	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs34852276	CHURC1	cis	Skin Sun Exposed Lower leg	GTEx
rs34852276	CHURC1	cis	lymphoblastoid	seeQTL
rs34852276	CHURC1	Cis_1M	lymphoblastoid	RTeQTL
rs34852276	RAB15	Cis_1M	lymphoblastoid	RTeQTL
rs34852276	CHURC1	cis	Artery Aorta	GTEx
rs34852276	CHURC1	cis	Muscle Skeletal	GTEx
rs34852276	CHURC1	cis	Whole Blood	GTEx
rs34852276	CHURC1	cis	Esophagus Muscularis	GTEx
rs34852276	RAB15	cis	lymphoblastoid	seeQTL
rs34852276	CHURC1	cis	Esophagus Mucosa	GTEx
rs34852276	CHURC1	cis	multi-tissue	Pritchard
rs34852276	CHURC1	cis	Nerve Tibial	GTEx
rs34852276	MAX	cis	cerebellum	SCAN
rs34852276	CHURC1	cis	Heart Left Ventricle	GTEx
rs34852276	CHURC1	cis	lung	GTEx
rs34852276	RAB15	cis	cerebellum	SCAN
rs34852276	CHURC1	cis	Adipose Subcutaneous	GTEx
rs34852276	CHURC1	cis	Artery Tibial	GTEx
rs34852276	CHURC1	cis	Thyroid	GTEx
rs34852276	CHURC1	cis	parietal	SCAN
rs34852276	CHURC1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65401400-65432200	Weak transcription	HUVEC	blood vessel
2	chr14:65401600-65435000	Weak transcription	NH-A	brain
3	chr14:65406600-65438000	Weak transcription	Fetal Kidney	kidney
4	chr14:65409600-65428400	Strong transcription	Fetal Stomach	stomach
5	chr14:65411000-65437200	Weak transcription	Fetal Lung	lung
6	chr14:65411200-65435000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr14:65411400-65435000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:65411400-65438000	Weak transcription	Small Intestine	intestine
9	chr14:65412400-65438000	Weak transcription	Brain Substantia Nigra	brain
10	chr14:65415400-65432400	Weak transcription	Ovary	ovary
11	chr14:65415400-65438200	Weak transcription	Aorta	Aorta
12	chr14:65415600-65437600	Weak transcription	Colonic Mucosa	Colon
13	chr14:65417600-65437200	Weak transcription	Adipose Nuclei	Adipose
14	chr14:65417800-65437600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr14:65418200-65428200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr14:65418200-65435400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:65418400-65435000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:65418800-65429400	Weak transcription	Fetal Intestine Large	intestine
19	chr14:65419000-65430400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:65419000-65432600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr14:65419000-65433400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:65419000-65434600	Weak transcription	Brain Hippocampus Middle	brain
23	chr14:65419000-65435400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:65419200-65433400	Weak transcription	Lung	lung
25	chr14:65419400-65436600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:65419400-65437800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:65419600-65437600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:65420200-65436600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr14:65420600-65430000	Weak transcription	GM12878-XiMat	blood
30	chr14:65420800-65430200	Weak transcription	Brain Anterior Caudate	brain
31	chr14:65420800-65437400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:65422000-65428400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr14:65422800-65437600	Weak transcription	Spleen	Spleen
34	chr14:65423400-65436800	Weak transcription	Dnd41	blood
35	chr14:65424000-65428400	Enhancers	Esophagus	oesophagus
36	chr14:65424000-65436800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr14:65424600-65429400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:65426000-65438200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr14:65426400-65428400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:65426600-65428400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr14:65426600-65428400	Enhancers	Fetal Muscle Trunk	muscle
42	chr14:65426600-65428600	Enhancers	Fetal Muscle Leg	muscle
43	chr14:65426800-65428200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr14:65427000-65428200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr14:65427000-65428200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr14:65427000-65428200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr14:65427000-65428200	Enhancers	HSMMtube	muscle
48	chr14:65427000-65428400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr14:65427000-65428400	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr14:65427000-65428400	Enhancers	Right Atrium	heart

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