Variant report

Variant	rs168633
Chromosome Location	chr3:138495759-138495760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138491131..138492639-chr3:138494759..138496280,2	MCF-7	breast:
2	chr3:138493707..138496520-chr3:138503545..138506035,2	K562	blood:
3	chr3:138489312..138491006-chr3:138494503..138496803,2	K562	blood:

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1066197	0.87[EUR][1000 genomes]
rs1068104	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1068685	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11705762	0.94[EUR][1000 genomes]
rs11709768	0.95[EUR][1000 genomes]
rs11713049	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11717457	0.90[EUR][1000 genomes]
rs11720178	0.88[EUR][1000 genomes]
rs11924814	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13069296	0.88[EUR][1000 genomes]
rs13082808	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13433948	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1400266	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1663556	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1673597	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs181729	0.88[EUR][1000 genomes]
rs187245	0.80[EUR][1000 genomes]
rs191713	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs191714	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs191775	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2197387	0.95[EUR][1000 genomes]
rs2348147	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs244380	0.94[EUR][1000 genomes]
rs244381	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2595928	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2595930	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2607796	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28376988	0.94[EUR][1000 genomes]
rs28408150	0.94[EUR][1000 genomes]
rs34354181	0.82[EUR][1000 genomes]
rs35214574	0.91[EUR][1000 genomes]
rs361054	0.94[EUR][1000 genomes]
rs361056	0.85[AFR][1000 genomes]
rs361057	0.87[EUR][1000 genomes]
rs361059	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361060	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361061	0.94[EUR][1000 genomes]
rs361062	0.94[EUR][1000 genomes]
rs361063	0.89[EUR][1000 genomes]
rs361064	0.82[AFR][1000 genomes]
rs361066	0.96[EUR][1000 genomes]
rs361067	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361068	0.96[EUR][1000 genomes]
rs361069	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs361071	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361072	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361079	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs361080	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361081	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361082	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361083	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361084	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361088	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361089	0.88[EUR][1000 genomes]
rs361092	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs361094	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs361097	0.88[EUR][1000 genomes]
rs371762	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs385254	0.94[EUR][1000 genomes]
rs398065	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs404110	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs409507	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs413147	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs425901	0.94[EUR][1000 genomes]
rs4305444	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs439720	0.93[EUR][1000 genomes]
rs448808	0.93[EUR][1000 genomes]
rs470359	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473388	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs475254	0.89[EUR][1000 genomes]
rs476800	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs482334	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894350	0.96[EUR][1000 genomes]
rs4894351	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4894352	0.96[EUR][1000 genomes]
rs4894353	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4894354	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs491371	0.95[EUR][1000 genomes]
rs497900	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs500687	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs511207	0.95[EUR][1000 genomes]
rs524164	0.89[EUR][1000 genomes]
rs539156	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs539619	0.96[EUR][1000 genomes]
rs540198	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs540907	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs550768	0.87[EUR][1000 genomes]
rs558905	0.96[EUR][1000 genomes]
rs559160	0.89[EUR][1000 genomes]
rs559451	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs564455	0.96[EUR][1000 genomes]
rs589986	0.87[EUR][1000 genomes]
rs603723	0.89[EUR][1000 genomes]
rs607044	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs618457	0.85[EUR][1000 genomes]
rs621204	0.87[EUR][1000 genomes]
rs62282169	0.87[EUR][1000 genomes]
rs624099	0.88[EUR][1000 genomes]
rs625468	0.89[EUR][1000 genomes]
rs635592	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439817	0.94[EUR][1000 genomes]
rs6439819	0.91[EUR][1000 genomes]
rs647972	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs654459	0.80[EUR][1000 genomes]
rs6776585	0.94[EUR][1000 genomes]
rs6781914	0.86[EUR][1000 genomes]
rs6784610	0.81[EUR][1000 genomes]
rs6794270	0.82[EUR][1000 genomes]
rs6795203	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6801207	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6810351	0.94[EUR][1000 genomes]
rs7612106	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7643722	0.94[EUR][1000 genomes]
rs772612	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs773045	0.89[EUR][1000 genomes]
rs773184	0.87[EUR][1000 genomes]
rs9821694	0.96[EUR][1000 genomes]
rs9822714	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9823213	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9832012	0.95[EUR][1000 genomes]
rs9834963	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9853819	0.96[EUR][1000 genomes]
rs9863481	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9864176	0.89[EUR][1000 genomes]
rs9874723	0.81[EUR][1000 genomes]
rs9877108	0.81[EUR][1000 genomes]
rs9879784	0.88[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
rs168633	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs168633	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL
rs168633	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
2	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:138488000-138497000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:138488000-138497200	Weak transcription	Gastric	stomach
5	chr3:138488000-138498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138488000-138499800	Weak transcription	Thymus	Thymus
7	chr3:138488000-138504600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
9	chr3:138488200-138497000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:138488200-138499600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:138488200-138499600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:138488200-138503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:138488400-138512200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:138489000-138511600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:138489200-138499200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:138489200-138500000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:138489200-138519200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:138489800-138499000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:138489800-138499200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:138490200-138499200	Weak transcription	Dnd41	blood
21	chr3:138490800-138495800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:138490800-138499200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:138490800-138499400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:138492400-138496800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:138492400-138515800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:138492600-138495800	Enhancers	NHEK	skin
27	chr3:138492600-138496200	Enhancers	NHLF	lung
28	chr3:138492600-138496400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:138492600-138496400	Enhancers	Fetal Muscle Leg	muscle
30	chr3:138492800-138496200	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:138492800-138496200	Enhancers	Brain Hippocampus Middle	brain
32	chr3:138493200-138496200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:138494000-138496200	Enhancers	Brain Substantia Nigra	brain
34	chr3:138494000-138496200	Enhancers	Placenta	Placenta
35	chr3:138494200-138496000	Weak transcription	GM12878-XiMat	blood
36	chr3:138494200-138505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:138494400-138495800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:138494400-138496200	Enhancers	Fetal Muscle Trunk	muscle
39	chr3:138494400-138496600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:138494400-138499600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:138494400-138500200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:138494400-138511600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:138494400-138511600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:138494600-138495800	Enhancers	NHDF-Ad	bronchial
45	chr3:138494600-138496000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:138494600-138496000	Weak transcription	HepG2	liver
47	chr3:138494600-138496400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:138494600-138496400	Enhancers	Brain Germinal Matrix	brain
49	chr3:138494600-138497200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:138494600-138497200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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