Variant report

Variant	rs4001806
Chromosome Location	chr12:32389965-32389966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2608402	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2608403	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326633	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326634	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326636	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326637	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4001807	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv541454	chr12:32371080-32401245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4001806	BICD1	cis	Thyroid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32364200-32390000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:32365000-32390000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:32365000-32390200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:32365600-32391200	Weak transcription	Fetal Brain Male	brain
5	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
6	chr12:32371000-32390000	Weak transcription	HSMMtube	muscle
7	chr12:32371000-32390200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:32371200-32390000	Weak transcription	Aorta	Aorta
9	chr12:32371200-32390000	Weak transcription	Brain Germinal Matrix	brain
10	chr12:32371200-32390000	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:32371200-32390000	Weak transcription	Left Ventricle	heart
12	chr12:32371200-32390000	Weak transcription	Thymus	Thymus
13	chr12:32371200-32390200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:32371200-32393200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:32371200-32393400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:32371200-32406800	Weak transcription	Primary T cells from cord blood	blood
17	chr12:32371600-32390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:32371600-32390000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:32371600-32390000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:32371600-32393000	Weak transcription	NH-A	brain
21	chr12:32371600-32393400	Weak transcription	NHDF-Ad	bronchial
22	chr12:32377400-32390000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:32377400-32390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:32377600-32390200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:32380000-32401000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:32380600-32390000	Weak transcription	Fetal Intestine Small	intestine
27	chr12:32380600-32393200	Weak transcription	Spleen	Spleen
28	chr12:32380800-32390200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:32381000-32390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:32381200-32390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:32381200-32390000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:32381200-32390200	Weak transcription	Primary B cells from cord blood	blood
33	chr12:32381200-32392800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:32381600-32390200	Weak transcription	Osteobl	bone
35	chr12:32383800-32390200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:32386400-32390000	Weak transcription	Ovary	ovary
37	chr12:32386800-32390000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:32386800-32394000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:32387000-32390200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:32388200-32390200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:32388200-32390600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:32388200-32390600	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:32388400-32390000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:32388400-32390200	Weak transcription	Brain Angular Gyrus	brain
45	chr12:32388600-32390200	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:32388800-32390000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:32389200-32391000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr12:32389400-32390000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:32389400-32390600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
50	chr12:32389400-32390600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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