Variant report

Variant	rs6794270
Chromosome Location	chr3:138536314-138536315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138536257..138538610-chr3:138539185..138541782,2	K562	blood:
2	chr3:138535838..138538762-chr3:138546948..138549872,2	K562	blood:

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10804659	0.86[EUR][1000 genomes]
rs10935288	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11705762	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706016	0.81[EUR][1000 genomes]
rs11708762	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709768	0.85[EUR][1000 genomes]
rs11711360	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713049	0.87[EUR][1000 genomes]
rs11720178	0.93[EUR][1000 genomes]
rs11924479	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924814	0.87[EUR][1000 genomes]
rs12497815	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631035	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12633714	0.83[EUR][1000 genomes]
rs13061496	0.81[EUR][1000 genomes]
rs13069296	0.80[EUR][1000 genomes]
rs13077455	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082808	0.88[EUR][1000 genomes]
rs1400266	0.87[EUR][1000 genomes]
rs1663556	0.81[EUR][1000 genomes]
rs168633	0.82[EUR][1000 genomes]
rs17484361	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181729	0.80[EUR][1000 genomes]
rs191713	0.84[EUR][1000 genomes]
rs191714	0.85[EUR][1000 genomes]
rs191775	0.83[EUR][1000 genomes]
rs2197387	0.85[EUR][1000 genomes]
rs244380	0.84[EUR][1000 genomes]
rs244381	0.80[EUR][1000 genomes]
rs2595930	0.80[EUR][1000 genomes]
rs28376988	0.84[EUR][1000 genomes]
rs28408150	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2881900	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35214574	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361054	0.84[EUR][1000 genomes]
rs361059	0.83[EUR][1000 genomes]
rs361060	0.84[EUR][1000 genomes]
rs361061	0.84[EUR][1000 genomes]
rs361062	0.84[EUR][1000 genomes]
rs361063	0.80[EUR][1000 genomes]
rs361066	0.85[EUR][1000 genomes]
rs361067	0.85[EUR][1000 genomes]
rs361068	0.85[EUR][1000 genomes]
rs361071	0.86[EUR][1000 genomes]
rs361072	0.85[EUR][1000 genomes]
rs361080	0.84[EUR][1000 genomes]
rs361081	0.84[EUR][1000 genomes]
rs361082	0.84[EUR][1000 genomes]
rs361083	0.84[EUR][1000 genomes]
rs361084	0.85[EUR][1000 genomes]
rs361092	0.81[EUR][1000 genomes]
rs361094	0.80[EUR][1000 genomes]
rs371762	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs385254	0.84[EUR][1000 genomes]
rs398065	0.86[EUR][1000 genomes]
rs404110	0.85[EUR][1000 genomes]
rs409507	0.84[EUR][1000 genomes]
rs413147	0.87[EUR][1000 genomes]
rs425901	0.81[EUR][1000 genomes]
rs4305444	0.84[EUR][1000 genomes]
rs439720	0.85[EUR][1000 genomes]
rs4405948	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448808	0.80[EUR][1000 genomes]
rs470359	0.80[EUR][1000 genomes]
rs473388	0.85[EUR][1000 genomes]
rs475254	0.81[EUR][1000 genomes]
rs476800	0.85[EUR][1000 genomes]
rs482334	0.86[EUR][1000 genomes]
rs4894350	0.85[EUR][1000 genomes]
rs4894351	0.85[EUR][1000 genomes]
rs4894352	0.85[EUR][1000 genomes]
rs4894353	0.85[EUR][1000 genomes]
rs4894354	0.84[EUR][1000 genomes]
rs4894358	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894359	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs491371	0.85[EUR][1000 genomes]
rs497900	0.83[EUR][1000 genomes]
rs500687	0.86[EUR][1000 genomes]
rs511207	0.85[EUR][1000 genomes]
rs524164	0.81[EUR][1000 genomes]
rs539156	0.80[EUR][1000 genomes]
rs539619	0.86[EUR][1000 genomes]
rs540198	0.85[EUR][1000 genomes]
rs540907	0.81[EUR][1000 genomes]
rs558905	0.86[EUR][1000 genomes]
rs559160	0.81[EUR][1000 genomes]
rs559451	0.81[EUR][1000 genomes]
rs564455	0.86[EUR][1000 genomes]
rs603723	0.81[EUR][1000 genomes]
rs607044	0.85[EUR][1000 genomes]
rs62282169	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs624099	0.80[EUR][1000 genomes]
rs625468	0.81[EUR][1000 genomes]
rs6439817	0.84[EUR][1000 genomes]
rs6439819	0.83[EUR][1000 genomes]
rs647972	0.85[EUR][1000 genomes]
rs6773514	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776585	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6780989	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784610	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791627	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795203	0.82[EUR][1000 genomes]
rs6800801	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801207	0.87[EUR][1000 genomes]
rs6810351	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7612106	0.88[EUR][1000 genomes]
rs7613579	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628172	0.85[EUR][1000 genomes]
rs7643722	0.84[EUR][1000 genomes]
rs7646689	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650967	0.86[EUR][1000 genomes]
rs772612	0.84[EUR][1000 genomes]
rs773045	0.81[EUR][1000 genomes]
rs9289566	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9647336	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9647337	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813576	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817727	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818354	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821694	0.86[EUR][1000 genomes]
rs9822500	0.83[EUR][1000 genomes]
rs9822714	0.86[EUR][1000 genomes]
rs9823213	0.82[EUR][1000 genomes]
rs9832012	0.85[EUR][1000 genomes]
rs9834963	0.87[EUR][1000 genomes]
rs9853819	0.81[EUR][1000 genomes]
rs9855727	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864176	0.81[EUR][1000 genomes]
rs9877108	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879784	0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6794270	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs6794270	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs6794270	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138494800-138537000	Weak transcription	HUVEC	blood vessel
2	chr3:138504000-138552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:138506000-138542200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:138506000-138551800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:138506400-138536800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:138506600-138537000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:138512000-138542800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:138512400-138536800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:138513400-138536800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:138513400-138544400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:138513600-138536600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:138513800-138543000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:138513800-138543000	Weak transcription	Placenta	Placenta
14	chr3:138514400-138536600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:138514800-138542600	Weak transcription	Hela-S3	cervix
16	chr3:138519400-138536600	Weak transcription	Left Ventricle	heart
17	chr3:138519400-138536600	Weak transcription	Psoas Muscle	Psoas
18	chr3:138522600-138536600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:138522600-138536800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:138522600-138537000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:138522800-138537000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:138522800-138537000	Weak transcription	Small Intestine	intestine
23	chr3:138523000-138542600	Weak transcription	HMEC	breast
24	chr3:138523000-138543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:138523400-138536600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:138525600-138536400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr3:138527400-138536600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:138527600-138536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:138527600-138537000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:138528800-138552600	Weak transcription	Colonic Mucosa	Colon
31	chr3:138529200-138536800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:138529400-138536600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:138529400-138536800	Weak transcription	A549	lung
34	chr3:138529400-138537400	Weak transcription	Fetal Intestine Large	intestine
35	chr3:138529400-138544400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:138530600-138539200	Weak transcription	Fetal Intestine Small	intestine
37	chr3:138531200-138542600	Weak transcription	Fetal Stomach	stomach
38	chr3:138531800-138537000	Weak transcription	Fetal Heart	heart
39	chr3:138531800-138542800	Weak transcription	Osteobl	bone
40	chr3:138532800-138537000	Strong transcription	K562	blood
41	chr3:138533200-138536800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:138533200-138542600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:138533600-138537000	Weak transcription	Lung	lung
44	chr3:138534600-138536600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:138534800-138536400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:138534800-138536600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:138534800-138536600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:138534800-138536800	Weak transcription	GM12878-XiMat	blood
49	chr3:138534800-138537000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:138535000-138536600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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