Variant report

Variant	rs9647336
Chromosome Location	chr3:138552705-138552706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138551363..138553278-chr3:138585364..138587238,2	K562	blood:
2	chr3:138541276..138545209-chr3:138550830..138554565,5	MCF-7	breast:
3	chr3:138552568..138555141-chr3:138666105..138668600,2	K562	blood:
4	chr3:138552259..138555153-chr3:138660631..138662853,2	K562	blood:
5	chr3:138312690..138314858-chr3:138552284..138553853,2	K562	blood:
6	chr3:138552263..138555163-chr3:138665790..138667540,3	K562	blood:

Variant related genes	Relation type
ENSG00000206262	Chromatin interaction
ENSG00000114107	Chromatin interaction
ENSG00000183770	Chromatin interaction
ENSG00000241429	Chromatin interaction
ENSG00000244578	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1068685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10804659	0.91[EUR][1000 genomes]
rs10935288	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706016	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11708762	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711360	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11720178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11924479	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12497815	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631035	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633714	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs13061496	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs13072146	0.83[EUR][1000 genomes]
rs13077455	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082808	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1400266	0.80[EUR][1000 genomes]
rs1663554	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1673597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs17484361	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs191714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs191775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs2607796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs2881900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs361057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs361061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs361067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs361071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs361072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs361080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs361087	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs361088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs361096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs385254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs404110	0.84[AFR][1000 genomes]
rs413147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4305444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4405948	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470359	0.87[YRI][hapmap]
rs4894351	0.83[AFR][1000 genomes]
rs4894353	0.82[AFR][1000 genomes]
rs4894358	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894359	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493152	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs497900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs500687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs520904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs524164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs531577	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs540198	0.84[AFR][1000 genomes]
rs558905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs559160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs564455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs603723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62282169	0.81[AMR][1000 genomes]
rs624099	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs635592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap]
rs6439817	1.00[CEU][hapmap]
rs6773514	0.96[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780989	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791627	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794270	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800801	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801207	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7613579	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628172	0.90[EUR][1000 genomes]
rs7643722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7646689	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650967	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs773045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9289566	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813576	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817727	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818354	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	1.00[CEU][hapmap]
rs9822500	0.88[EUR][1000 genomes]
rs9822714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9834963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9851887	0.83[EUR][1000 genomes]
rs9855727	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9877108	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer 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	38 gene(s)	inside rSNPs	diseases
2	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9647336	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs9647336	CEP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138551200-138554000	Active TSS	K562	blood
2	chr3:138551400-138554000	Active TSS	Placenta	Placenta
3	chr3:138551600-138552800	Weak transcription	Small Intestine	intestine
4	chr3:138551600-138553000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:138551600-138554200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:138551600-138554400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:138551800-138554400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:138552000-138552800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:138552000-138553000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:138552000-138553200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr3:138552000-138553200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:138552000-138554000	Active TSS	NHLF	lung
13	chr3:138552000-138554200	Active TSS	Brain Hippocampus Middle	brain
14	chr3:138552000-138554200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:138552200-138552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:138552200-138552800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:138552200-138552800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:138552200-138552800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr3:138552200-138552800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr3:138552200-138552800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:138552200-138552800	Flanking Active TSS	Thymus	Thymus
22	chr3:138552200-138552800	Flanking Active TSS	Hela-S3	cervix
23	chr3:138552200-138552800	Flanking Active TSS	HMEC	breast
24	chr3:138552200-138553000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr3:138552200-138553000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:138552200-138553000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:138552200-138553000	Flanking Active TSS	Liver	Liver
28	chr3:138552200-138553000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr3:138552200-138553000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr3:138552200-138553000	Flanking Active TSS	HUVEC	blood vessel
31	chr3:138552200-138553000	Flanking Active TSS	Osteobl	bone
32	chr3:138552200-138553200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr3:138552200-138553200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:138552200-138553200	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr3:138552200-138553200	Flanking Active TSS	Dnd41	blood
36	chr3:138552200-138553200	Flanking Active TSS	NHEK	skin
37	chr3:138552200-138553400	Active TSS	Right Atrium	heart
38	chr3:138552200-138553600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:138552200-138554000	Active TSS	GM12878-XiMat	blood
40	chr3:138552200-138554200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:138552200-138554200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr3:138552200-138554200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr3:138552200-138554200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:138552200-138554200	Active TSS	Fetal Kidney	kidney
45	chr3:138552200-138554400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:138552200-138554400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:138552400-138552800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr3:138552400-138552800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr3:138552400-138552800	Flanking Active TSS	Fetal Brain Female	brain
50	chr3:138552400-138552800	Flanking Active TSS	Fetal Lung	lung

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