Variant report

Variant	rs12421865
Chromosome Location	chr11:18742043-18742044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18741015..18744617-chr11:18749870..18752348,3	K562	blood:
2	chr11:18725792..18727506-chr11:18741119..18743990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110786	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11024770	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605980	0.89[YRI][hapmap]
rs12417433	0.93[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs12418990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35185666	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv897028	chr11:18714623-18770822	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv525192	chr11:18722791-18793360	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1047371	chr11:18731473-18763037	Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv525452	chr11:18735947-18802503	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12421865	SOX6	cis	cerebellum	SCAN
rs12421865	TPH1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18728400-18742200	Weak transcription	Gastric	stomach
2	chr11:18728600-18742200	Weak transcription	Right Ventricle	heart
3	chr11:18728600-18742600	Weak transcription	Aorta	Aorta
4	chr11:18728800-18742400	Weak transcription	Fetal Kidney	kidney
5	chr11:18729000-18742200	Weak transcription	Ovary	ovary
6	chr11:18735400-18742200	Weak transcription	Brain Anterior Caudate	brain
7	chr11:18735800-18742200	Weak transcription	Pancreas	Pancrea
8	chr11:18736600-18742200	Weak transcription	Spleen	Spleen
9	chr11:18737800-18742200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:18740000-18742200	Weak transcription	Brain Germinal Matrix	brain
11	chr11:18741200-18742200	Enhancers	Fetal Intestine Small	intestine
12	chr11:18741400-18742200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:18741400-18742400	Enhancers	Fetal Intestine Large	intestine
14	chr11:18741600-18742200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:18741600-18742200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:18741600-18742400	Enhancers	Brain Angular Gyrus	brain
17	chr11:18741600-18742400	Enhancers	Fetal Muscle Leg	muscle
18	chr11:18741600-18742800	Enhancers	Small Intestine	intestine
19	chr11:18741800-18742200	Enhancers	Fetal Lung	lung
20	chr11:18741800-18742200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr11:18741800-18742200	Enhancers	Osteobl	bone
22	chr11:18741800-18742400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:18741800-18742400	Enhancers	Colon Smooth Muscle	Colon
24	chr11:18741800-18742400	Enhancers	Fetal Stomach	stomach
25	chr11:18741800-18742600	Bivalent Enhancer	HepG2	liver
26	chr11:18742000-18742200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:18742000-18742200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr11:18742000-18742200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:18742000-18742200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:18742000-18742200	Enhancers	Adipose Nuclei	Adipose
31	chr11:18742000-18742200	Enhancers	Brain Hippocampus Middle	brain
32	chr11:18742000-18742200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr11:18742000-18742200	Active TSS	Rectal Smooth Muscle	rectum
34	chr11:18742000-18742400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr11:18742000-18742400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:18742000-18742400	Enhancers	Brain Cingulate Gyrus	brain
37	chr11:18742000-18742400	Enhancers	Fetal Brain Female	brain
38	chr11:18742000-18742400	Enhancers	Fetal Muscle Trunk	muscle
39	chr11:18742000-18743800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr11:18742000-18744000	Active TSS	Fetal Brain Male	brain

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