Variant report

Variant	rs9681209
Chromosome Location	chr3:121491112-121491113
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121467285..121470096-chr3:121490957..121493415,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10934560	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489511	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490565	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067629	0.95[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1492177	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs1574655	0.83[EUR][1000 genomes]
rs1574735	0.83[EUR][1000 genomes]
rs17849995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873645	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs1919552	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1919557	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2001390	0.83[EUR][1000 genomes]
rs2001391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs2070179	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs2141614	0.90[JPT][hapmap]
rs2332056	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs2840143	0.90[CEU][hapmap];0.83[CHB][hapmap]
rs34920680	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34980632	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35713885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022362	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676689	0.82[EUR][1000 genomes]
rs4676690	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4676751	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4676754	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57420306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59740137	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438661	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771716	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6774164	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776703	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6791510	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6794341	0.83[EUR][1000 genomes]
rs6802033	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs6803839	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs6807711	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs73179983	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7375038	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs7429247	0.86[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs7611913	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs7646346	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]
rs7646585	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs9289172	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs9289173	0.91[CEU][hapmap];0.85[CHB][hapmap]
rs9681049	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809114	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs9812411	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs9829053	0.83[EUR][1000 genomes]
rs9832267	0.80[EUR][1000 genomes]
rs9835182	0.83[EUR][1000 genomes]
rs9854052	0.80[EUR][1000 genomes]
rs9864907	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs9876021	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	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
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv933820	chr3:121489302-121500759	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9681209	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9681209	HCLS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121477200-121494000	Weak transcription	Right Ventricle	heart
2	chr3:121478000-121499400	Weak transcription	HepG2	liver
3	chr3:121483600-121498600	Weak transcription	Fetal Kidney	kidney
4	chr3:121483800-121498400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:121484400-121494000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:121484600-121499000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:121485400-121493200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:121485600-121497200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:121485600-121503200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:121485800-121501000	Strong transcription	Duodenum Mucosa	Duodenum
11	chr3:121486000-121491400	Weak transcription	NHLF	lung
12	chr3:121486200-121491200	Weak transcription	NHEK	skin
13	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
14	chr3:121486800-121496000	Weak transcription	Hela-S3	cervix
15	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:121487000-121494000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:121487000-121498800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:121487000-121509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:121487200-121501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:121487400-121491600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:121487400-121491600	Strong transcription	NHDF-Ad	bronchial
22	chr3:121487400-121492000	Strong transcription	Adipose Nuclei	Adipose
23	chr3:121487400-121492600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:121487400-121493000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:121487400-121493400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:121487400-121494200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:121487400-121494800	Strong transcription	HSMM	muscle
28	chr3:121487400-121495200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:121487400-121497200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:121487400-121499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:121487400-121501400	Strong transcription	Primary T cells from cord blood	blood
32	chr3:121487400-121501400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:121487400-121502000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:121487400-121503000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:121487400-121512200	Strong transcription	Fetal Thymus	thymus
36	chr3:121487400-121512400	Strong transcription	Dnd41	blood
37	chr3:121487600-121495600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:121487600-121497200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:121487600-121498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:121487800-121491600	Strong transcription	Placenta	Placenta
41	chr3:121487800-121497600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:121487800-121509000	Strong transcription	Fetal Intestine Large	intestine
43	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:121488000-121492000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:121488000-121507200	Weak transcription	Brain Substantia Nigra	brain
47	chr3:121488000-121511000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:121488000-121512200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:121488000-121512600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:121488200-121493800	Strong transcription	Primary B cells from cord blood	blood

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