Variant report

Variant	rs7646346
Chromosome Location	chr3:121552228-121552229
allele	G/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	KAP1	chr3:121552210-121552627	K562	blood:	n/a	chr3:121552256-121552264 chr3:121552585-121552593
2	POLR2A	chr3:121551766-121552542	K562	blood:	n/a	n/a
3	CTCF	chr3:121552140-121552290	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121540007..121542032-chr3:121549979..121552263,2	K562	blood:
2	chr3:121552093..121553677-chr3:122102440..122104911,2	K562	blood:
3	chr3:121523456..121525541-chr3:121550635..121553696,3	K562	blood:

Variant related genes	Relation type
EAF2	TF binding region
ENSG00000114023	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10934560	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934568	0.82[CHB][hapmap]
rs12489511	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490565	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13067629	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs17849995	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1919552	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs1919557	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2001391	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2070179	0.85[CEU][hapmap];0.92[CHB][hapmap]
rs2332056	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2700424	0.82[CHB][hapmap]
rs34227248	0.92[ASN][1000 genomes]
rs34920680	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34980632	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35713885	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36022362	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4676690	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4676751	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4676754	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57420306	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59740137	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6438660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6438661	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770719	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771716	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6774164	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6776703	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6791510	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6802033	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs6803839	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs6807711	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs73179983	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73181839	0.95[ASN][1000 genomes]
rs7429247	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs7646585	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs7652239	0.95[ASN][1000 genomes]
rs9289172	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs9289173	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs9681049	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9681209	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9809114	0.85[CEU][hapmap];0.92[CHB][hapmap]
rs9812411	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs9829053	0.80[EUR][1000 genomes]
rs9864907	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs9876021	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv933192	chr3:121544496-121575871	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7646346	EAF2	cis	multi-tissue	Pritchard
rs7646346	HCLS1	Cis_1M	lymphoblastoid	RTeQTL
rs7646346	HCLS1	cis	multi-tissue	Pritchard
rs7646346	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121491600-121552600	Weak transcription	NHLF	lung
2	chr3:121528000-121553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:121530800-121552400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:121530800-121552800	Weak transcription	HSMMtube	muscle
5	chr3:121530800-121553000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:121530800-121553200	Weak transcription	Esophagus	oesophagus
7	chr3:121531000-121552800	Weak transcription	Fetal Stomach	stomach
8	chr3:121531000-121552800	Weak transcription	Pancreas	Pancrea
9	chr3:121531000-121552800	Weak transcription	Right Ventricle	heart
10	chr3:121531000-121552800	Weak transcription	Spleen	Spleen
11	chr3:121536200-121552800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:121537200-121552600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:121537400-121552800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:121539800-121552600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:121539800-121552600	Strong transcription	HSMM	muscle
16	chr3:121541200-121553000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:121541400-121552800	Weak transcription	Aorta	Aorta
18	chr3:121541600-121552800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:121542200-121552800	Weak transcription	Left Ventricle	heart
20	chr3:121542800-121553200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:121543000-121553400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:121543200-121552600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:121543200-121552800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:121543200-121552800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:121543200-121553200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:121543200-121553200	Weak transcription	Lung	lung
27	chr3:121543400-121552400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:121544000-121553000	Weak transcription	Ovary	ovary
29	chr3:121544400-121553200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:121545400-121552400	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:121545600-121552600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:121545600-121552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:121545600-121552800	Weak transcription	Fetal Brain Male	brain
34	chr3:121546400-121552800	Weak transcription	Colonic Mucosa	Colon
35	chr3:121546600-121552600	Weak transcription	Brain Anterior Caudate	brain
36	chr3:121546600-121552600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:121546800-121552800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:121547200-121552400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:121547200-121552600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:121547400-121552800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:121547400-121552800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:121547400-121552800	Weak transcription	Fetal Brain Female	brain
43	chr3:121547400-121552800	Weak transcription	Fetal Kidney	kidney
44	chr3:121547400-121552800	Weak transcription	NH-A	brain
45	chr3:121547600-121552800	Weak transcription	Adipose Nuclei	Adipose
46	chr3:121548000-121552800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:121548200-121552800	Weak transcription	Liver	Liver
48	chr3:121548200-121553000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:121548600-121552400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:121548600-121552800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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