Variant report

Variant	rs6574651
Chromosome Location	chr14:81865426-81865427
allele	A/G
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	chr14:81865001-81865771	MCF-7	breast:	n/a	chr14:81865113-81865129
2	PRDM1	chr14:81865136-81865459	Hela-S3	cervix:	n/a	chr14:81865258-81865272 chr14:81865259-81865272 chr14:81865263-81865278 chr14:81865264-81865278 chr14:81865265-81865274
3	GATA3	chr14:81865284-81865548	T-47D	breast:	n/a	n/a
4	GATA3	chr14:81865105-81865568	SH-SY5Y	brain:	n/a	chr14:81865113-81865129
5	MYC	chr14:81865214-81865440	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr14:81865064-81865704	MCF-7	breast:	n/a	chr14:81865113-81865129

No.	Distal block	Cell Line	Cell type
1	chr14:81864941..81867433-chr14:81921571..81923631,2	K562	blood:
2	chr14:81865287..81867829-chr14:81917916..81919892,2	K562	blood:
3	chr14:81865299..81866947-chr14:81897451..81900314,2	K562	blood:

Variant related genes	Relation type
STON2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1003258	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10135926	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10146094	0.82[AMR][1000 genomes]
rs10147416	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10148622	0.82[TSI][hapmap];0.85[YRI][hapmap]
rs12588572	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs1569012	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17111790	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs2145123	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2371596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2371599	0.81[CHB][hapmap]
rs2371602	0.81[CHB][hapmap]
rs28476767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825606	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3844533	0.86[ASN][1000 genomes]
rs3844534	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs3853419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3853420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3853421	0.87[ASN][1000 genomes]
rs3915222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4110459	0.86[ASN][1000 genomes]
rs4110460	0.88[ASN][1000 genomes]
rs4110462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4275784	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4290414	0.91[CHB][hapmap];0.85[LWK][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4903982	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574649	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574650	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574653	0.81[CHB][hapmap]
rs7153104	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7153556	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7153600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7160907	0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72703752	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72703760	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8018198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8020806	0.88[ASN][1000 genomes]
rs8022070	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs9652383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3358936	chr14:81786719-81928269	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv902119	chr14:81810945-81884857	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1047694	chr14:81831147-82534026	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv542145	chr14:81831147-82534026	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6574651	STON2	cis	cerebellum	SCAN
rs6574651	NGB	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81836400-81885800	Weak transcription	Gastric	stomach
2	chr14:81852800-81899800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:81853200-81866400	Weak transcription	Brain Substantia Nigra	brain
4	chr14:81853200-81866600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:81855000-81866000	Strong transcription	K562	blood
6	chr14:81858200-81865600	Weak transcription	Fetal Brain Female	brain
7	chr14:81858200-81867000	Weak transcription	Brain Germinal Matrix	brain
8	chr14:81859400-81866800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:81860000-81866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:81860200-81867400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr14:81861000-81873000	Weak transcription	HepG2	liver
12	chr14:81861200-81866400	Weak transcription	Brain Angular Gyrus	brain
13	chr14:81861400-81869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr14:81861400-81889400	Weak transcription	Fetal Kidney	kidney
15	chr14:81861600-81873200	Weak transcription	Brain Hippocampus Middle	brain
16	chr14:81861800-81866400	Weak transcription	Adipose Nuclei	Adipose
17	chr14:81861800-81866600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:81862800-81866200	Weak transcription	NHLF	lung
19	chr14:81862800-81866400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:81862800-81867000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:81862800-81867800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr14:81862800-81881400	Weak transcription	Fetal Intestine Small	intestine
23	chr14:81863000-81866200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr14:81863000-81866200	Weak transcription	Placenta	Placenta
25	chr14:81863400-81866200	Weak transcription	HSMMtube	muscle
26	chr14:81864200-81866200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr14:81864200-81866400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr14:81864400-81866400	Weak transcription	Brain Anterior Caudate	brain
29	chr14:81864400-81867000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:81864400-81867200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr14:81864400-81893600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr14:81864600-81866200	Enhancers	Hela-S3	cervix
33	chr14:81864600-81866200	Enhancers	HMEC	breast
34	chr14:81864600-81867000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:81864600-81870000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:81864800-81866200	Weak transcription	Psoas Muscle	Psoas
37	chr14:81864800-81866200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr14:81864800-81866600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:81864800-81866800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr14:81864800-81867400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr14:81864800-81869200	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr14:81865000-81865600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr14:81865000-81866000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr14:81865000-81866200	Weak transcription	Esophagus	oesophagus
45	chr14:81865000-81866400	Weak transcription	Fetal Muscle Leg	muscle
46	chr14:81865000-81866400	Weak transcription	Spleen	Spleen
47	chr14:81865000-81866800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:81865000-81867200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr14:81865000-81869400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:81865000-81884600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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