Variant report

Variant	rs7945639
Chromosome Location	chr11:3942001-3942002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr11:3940684-3942172	K562	blood:	n/a	chr11:3940783-3940793 chr11:3940783-3940792 chr11:3940783-3940793
2	EP300	chr11:3941389-3942020	GM12878	blood:	n/a	n/a
3	ZNF384	chr11:3941841-3942124	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3941075..3943493-chr11:3946471..3948853,2	K562	blood:
2	chr11:3844015..3846583-chr11:3941327..3942924,2	K562	blood:

Variant related genes	Relation type
ENSG00000206976	TF binding region
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10835301	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030224	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs11030264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030394	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030842	0.82[CHB][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs12803023	0.81[MKK][hapmap]
rs1372804	0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs1372805	0.83[MKK][hapmap]
rs17193797	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304891	0.83[MKK][hapmap]
rs2735691	0.81[MKK][hapmap]
rs2920144	0.84[GIH][hapmap]
rs2923944	0.96[CEU][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2923945	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2923956	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2958713	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2958714	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959056	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2959068	0.81[MKK][hapmap]
rs2959070	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2959075	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2959081	0.92[CEU][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]
rs34662040	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910863	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7938196	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3916600-3943800	Weak transcription	Fetal Stomach	stomach
2	chr11:3916600-3948800	Weak transcription	Aorta	Aorta
3	chr11:3924000-3950600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:3927200-3942600	Weak transcription	Spleen	Spleen
5	chr11:3927600-3943600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:3929400-3950600	Weak transcription	Ovary	ovary
7	chr11:3931600-3942600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr11:3932200-3942800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:3932400-3944000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr11:3934800-3951000	Weak transcription	Gastric	stomach
11	chr11:3935400-3942400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr11:3935400-3943000	Weak transcription	Fetal Lung	lung
13	chr11:3935400-3944000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:3935600-3942600	Enhancers	Primary B cells from peripheral blood	blood
15	chr11:3935600-3943200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr11:3935600-3943400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:3936000-3943200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr11:3936000-3943600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:3937800-3950600	Weak transcription	Lung	lung
20	chr11:3938400-3956400	Weak transcription	Dnd41	blood
21	chr11:3938600-3949800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:3939000-3950200	Weak transcription	Left Ventricle	heart
23	chr11:3939000-3950200	Weak transcription	Pancreas	Pancrea
24	chr11:3939000-3956000	Weak transcription	Esophagus	oesophagus
25	chr11:3939200-3942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:3939400-3947200	Weak transcription	Liver	Liver
27	chr11:3939600-3947800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:3939600-3948800	Weak transcription	Thymus	Thymus
29	chr11:3939600-3950000	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:3939600-3950200	Weak transcription	Fetal Thymus	thymus
31	chr11:3940000-3947400	Weak transcription	Psoas Muscle	Psoas
32	chr11:3940200-3942200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:3940200-3947800	Weak transcription	HepG2	liver
34	chr11:3940800-3942200	Enhancers	HMEC	breast
35	chr11:3940800-3942600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:3940800-3943400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr11:3941200-3944000	Weak transcription	HUVEC	blood vessel
38	chr11:3941200-3948600	Weak transcription	Right Ventricle	heart
39	chr11:3941600-3942400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:3941600-3942600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:3941600-3942600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:3941600-3942600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:3941600-3943800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr11:3941600-3947800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:3941600-3948000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:3941600-3950600	Weak transcription	Stomach Mucosa	stomach
47	chr11:3941600-3951000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:3941800-3942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:3942000-3942600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:3942000-3942600	Weak transcription	Primary B cells from cord blood	blood

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