Variant report

Variant	rs12090246
Chromosome Location	chr1:151107496-151107497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151107196-151107865	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151106109..151108676-chr1:151117941..151119953,3	K562	blood:
2	chr1:151106923..151108713-chr1:151252226..151254110,2	K562	blood:
3	chr1:151104790..151107252-chr1:151107376..151109485,2	K562	blood:
4	chr1:151106109..151110392-chr1:151117941..151122227,5	K562	blood:
5	chr1:150980411..150982537-chr1:151106245..151107794,2	K562	blood:
6	chr1:151106097..151107684-chr1:151136573..151139445,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261168	TF binding region
SEMA6C	TF binding region
ENSG00000163155	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11204755	0.84[CEU][hapmap]
rs11204774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11204783	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs12058128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12060682	0.96[EUR][1000 genomes]
rs12065634	0.86[YRI][hapmap]
rs12067174	1.00[ASW][hapmap];0.81[LWK][hapmap]
rs12068365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs12070256	0.81[EUR][1000 genomes]
rs12074309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12078857	0.82[ASW][hapmap];0.93[YRI][hapmap]
rs12088079	0.86[YRI][hapmap]
rs12088941	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes]
rs12089658	0.82[ASW][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs12097169	0.86[EUR][1000 genomes]
rs16832976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs34761930	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3892218	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59603391	0.94[EUR][1000 genomes]
rs61321900	0.86[EUR][1000 genomes]
rs6587556	0.89[AFR][1000 genomes]
rs6664387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs6689566	1.00[GIH][hapmap]
rs7526955	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7537292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs955955	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151114800	Weak transcription	HSMM	muscle
2	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
3	chr1:151104200-151107800	Weak transcription	Liver	Liver
4	chr1:151104400-151107600	Weak transcription	GM12878-XiMat	blood
5	chr1:151104400-151110400	Weak transcription	NHLF	lung
6	chr1:151104400-151111200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
9	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
10	chr1:151104600-151107600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:151104600-151108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:151104600-151109000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
15	chr1:151104800-151107600	Weak transcription	Lung	lung
16	chr1:151104800-151108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:151104800-151108400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
20	chr1:151105000-151114800	Weak transcription	Right Atrium	heart
21	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
23	chr1:151105200-151108200	Weak transcription	Esophagus	oesophagus
24	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
27	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:151105600-151112800	Strong transcription	Left Ventricle	heart
29	chr1:151105600-151114800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:151105600-151118000	Weak transcription	Gastric	stomach
32	chr1:151105800-151113000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:151105800-151115600	Weak transcription	Thymus	Thymus
34	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
35	chr1:151106000-151109200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:151106000-151111000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:151106000-151112200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:151106000-151113200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:151106000-151113200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:151106000-151113400	Strong transcription	Fetal Intestine Large	intestine
41	chr1:151106000-151114800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:151106000-151115000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:151106200-151108000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:151106200-151110600	Strong transcription	HSMMtube	muscle
45	chr1:151106200-151110800	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:151106200-151110800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr1:151106200-151113000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:151106200-151113000	Strong transcription	Fetal Lung	lung
49	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr1:151106400-151107800	Strong transcription	Fetal Muscle Trunk	muscle

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