Variant report

Variant	rs3806386
Chromosome Location	chr1:151031667-151031668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150951870..150954741-chr1:151030040..151032027,2	K562	blood:
2	chr1:150976422..150979249-chr1:151029519..151032163,2	MCF-7	breast:
3	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
4	chr1:150549378..150552816-chr1:151028901..151032004,3	K562	blood:
5	chr1:150946136..150947648-chr1:151031480..151034167,2	MCF-7	breast:
6	chr1:150954707..150956253-chr1:151031263..151032998,2	MCF-7	breast:
7	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
8	chr1:150980774..150986118-chr1:151028117..151032528,6	MCF-7	breast:
9	chr1:151030654..151033886-chr1:151224560..151228363,4	MCF-7	breast:
10	chr1:150979106..150980954-chr1:151030690..151033653,4	K562	blood:
11	chr1:151029387..151032698-chr1:151136625..151139017,3	K562	blood:
12	chr1:150335804..150338048-chr1:151030580..151033260,2	MCF-7	breast:
13	chr1:150979291..150984938-chr1:151030285..151033653,10	K562	blood:
14	chr1:151030501..151032786-chr14:69259959..69262538,2	MCF-7	breast:
15	chr1:150943422..150945892-chr1:151029810..151031687,2	MCF-7	breast:
16	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
17	chr1:150898462..150900740-chr1:151030523..151033024,2	MCF-7	breast:
18	chr1:151029301..151033715-chr1:151136820..151141213,5	MCF-7	breast:
19	chr1:151030606..151033424-chr1:151127257..151129173,3	MCF-7	breast:
20	chr1:150976003..150979092-chr1:151029150..151032179,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000231073	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10749659	0.82[EUR][1000 genomes]
rs10788798	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10788799	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11204777	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11204778	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11204780	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11204782	0.82[JPT][hapmap]
rs12039334	0.82[EUR][1000 genomes]
rs12039542	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12117163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1524773	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1969442	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2140709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2902810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35550545	0.84[ASN][1000 genomes]
rs3738481	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806387	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357530	0.83[CHD][hapmap]
rs4970939	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4970941	0.88[CHD][hapmap]
rs4970990	0.82[ASN][1000 genomes]
rs4970993	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4970998	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs4971005	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs4971007	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4971008	0.94[CHD][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs6587552	0.81[CHD][hapmap]
rs6587553	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6657593	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668894	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6676190	0.83[CHD][hapmap]
rs6694158	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7366148	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7532312	1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs7540258	1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs7550434	1.00[CHB][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3806386	BNIPL	cis	lung	GTEx
rs3806386	CDC42SE1	cis	parietal	SCAN
rs3806386	BNIPL	cis	Thyroid	GTEx
rs3806386	CDC42SE1	cis	lymphoblastoid	seeQTL
rs3806386	CDC42SE1	cis	multi-tissue	Pritchard
rs3806386	PRPF3	cis	parietal	SCAN
rs3806386	MRPS21	cis	parietal	SCAN
rs3806386	ARNT	cis	parietal	SCAN
rs3806386	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs3806386	MRPS21	cis	cerebellum	SCAN
rs3806386	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs3806386	RPTN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151027200-151032000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
2	chr1:151028400-151031800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:151028400-151031800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:151028800-151033400	Active TSS	Primary T killer memory cells from peripheral blood	blood
5	chr1:151029400-151033200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:151029600-151032400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:151029600-151032400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:151029600-151032600	Active TSS	Primary T cells from cord blood	blood
9	chr1:151029600-151032600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr1:151029600-151033200	Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:151029800-151032400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:151030000-151031800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:151030000-151031800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr1:151030000-151032400	Active TSS	Small Intestine	intestine
15	chr1:151030200-151032200	Active TSS	Primary T cells fromperipheralblood	blood
16	chr1:151030200-151032400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:151030200-151035600	Active TSS	HSMMtube	muscle
18	chr1:151030400-151032400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
19	chr1:151030400-151032400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:151030400-151033200	Active TSS	Aorta	Aorta
21	chr1:151030400-151034200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:151030400-151034400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:151030600-151032400	Active TSS	GM12878-XiMat	blood
24	chr1:151030600-151034800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:151030600-151035200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:151030800-151031800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:151030800-151032200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:151030800-151032200	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr1:151030800-151032200	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:151030800-151032400	Active TSS	Primary B cells from peripheral blood	blood
31	chr1:151030800-151032400	Active TSS	Spleen	Spleen
32	chr1:151030800-151032800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:151030800-151032800	Active TSS	HMEC	breast
34	chr1:151030800-151033000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:151030800-151033000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:151030800-151033000	Active TSS	Lung	lung
37	chr1:151030800-151033200	Active TSS	Colon Smooth Muscle	Colon
38	chr1:151030800-151033400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:151030800-151033400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:151030800-151033600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:151030800-151033800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:151030800-151033800	Active TSS	Right Atrium	heart
43	chr1:151030800-151034000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:151030800-151034000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:151030800-151034200	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:151030800-151034200	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:151030800-151034400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:151030800-151034400	Active TSS	NHLF	lung
49	chr1:151030800-151034600	Active TSS	Thymus	Thymus
50	chr1:151030800-151034800	Active TSS	HUES48 Cell Line	embryonic stem cell

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