Variant report

Variant	rs12227868
Chromosome Location	chr12:76242802-76242803
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	chr12:76242079..76243789-chr12:76420036..76421626,2	MCF-7	breast:
2	chr12:76242367..76248604-chr12:76422405..76426784,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10879992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11180710	0.85[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs11180712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180714	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229980	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426679	0.85[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12426691	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1463754	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493791	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1493792	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1493794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493795	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532293	0.81[CEU][hapmap]
rs1565765	0.85[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs34439598	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35080799	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12227868	BBS10	cis	cerebellum	SCAN
rs12227868	OSBPL8	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76228600-76250000	Weak transcription	Pancreas	Pancrea
2	chr12:76239600-76244600	Weak transcription	HepG2	liver
3	chr12:76240400-76247400	Weak transcription	Aorta	Aorta
4	chr12:76240800-76244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:76241200-76243800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:76241200-76244000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:76241400-76243200	Enhancers	HUVEC	blood vessel
8	chr12:76241400-76243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:76241400-76243800	Enhancers	Fetal Stomach	stomach
10	chr12:76241400-76244000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:76241600-76243600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:76241600-76243600	Enhancers	Ovary	ovary
13	chr12:76241600-76243800	Enhancers	Fetal Muscle Leg	muscle
14	chr12:76241600-76246000	Enhancers	Brain Germinal Matrix	brain
15	chr12:76241600-76248800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:76241600-76251000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:76241800-76243800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:76242000-76243200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:76242000-76243200	Enhancers	Brain Anterior Caudate	brain
20	chr12:76242000-76243200	Enhancers	Brain Cingulate Gyrus	brain
21	chr12:76242000-76243200	Enhancers	Right Ventricle	heart
22	chr12:76242000-76243400	Enhancers	Brain Angular Gyrus	brain
23	chr12:76242000-76243400	Enhancers	Fetal Kidney	kidney
24	chr12:76242000-76243600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:76242000-76243600	Enhancers	HMEC	breast
26	chr12:76242000-76244000	Enhancers	Colon Smooth Muscle	Colon
27	chr12:76242000-76245400	Enhancers	NHLF	lung
28	chr12:76242000-76246600	Enhancers	Osteobl	bone
29	chr12:76242000-76247600	Enhancers	NHDF-Ad	bronchial
30	chr12:76242000-76249000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:76242200-76243200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:76242200-76243600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:76242200-76245200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:76242200-76245800	Enhancers	NHEK	skin
35	chr12:76242200-76247800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:76242400-76243000	Enhancers	Fetal Brain Female	brain
37	chr12:76242400-76243200	Enhancers	HSMMtube	muscle
38	chr12:76242400-76243400	Enhancers	Psoas Muscle	Psoas
39	chr12:76242400-76243800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr12:76242400-76243800	Enhancers	Rectal Smooth Muscle	rectum
41	chr12:76242600-76243000	Enhancers	Fetal Brain Male	brain
42	chr12:76242600-76243200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:76242600-76243200	Enhancers	Left Ventricle	heart
44	chr12:76242600-76243400	Enhancers	Brain Hippocampus Middle	brain
45	chr12:76242600-76244200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:76242600-76244400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:76242800-76243000	Flanking Active TSS	Fetal Lung	lung
48	chr12:76242800-76243200	Enhancers	Adipose Nuclei	Adipose
49	chr12:76242800-76243200	Enhancers	Brain Substantia Nigra	brain
50	chr12:76242800-76243800	Enhancers	Stomach Mucosa	stomach

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