Variant report

Variant	rs3759199
Chromosome Location	chr12:29657316-29657317
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29656485..29658831-chr12:29660611..29662823,3	K562	blood:

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3858549	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv469190	chr12:29612425-29811471	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv557917	chr12:29612425-29811471	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3759199	BICD1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29598400-29657400	Weak transcription	HSMM	muscle
2	chr12:29600600-29675600	Weak transcription	Psoas Muscle	Psoas
3	chr12:29613600-29666800	Weak transcription	Spleen	Spleen
4	chr12:29614600-29658000	Weak transcription	HSMMtube	muscle
5	chr12:29616400-29659400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:29617400-29657400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:29628000-29662000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:29638400-29666600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:29640000-29669200	Weak transcription	Brain Anterior Caudate	brain
10	chr12:29642400-29660200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:29649200-29659600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:29649600-29659200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:29650400-29699000	Weak transcription	Right Ventricle	heart
14	chr12:29652200-29659400	Weak transcription	Ovary	ovary
15	chr12:29652200-29673200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:29653000-29659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:29653400-29661200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:29653400-29672200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:29653800-29657400	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:29654000-29666600	Weak transcription	Fetal Kidney	kidney
21	chr12:29654000-29667000	Weak transcription	Fetal Stomach	stomach
22	chr12:29654000-29668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:29654000-29669200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:29654000-29669200	Weak transcription	NHLF	lung
25	chr12:29654200-29666800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:29654600-29669000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:29655200-29669400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:29655400-29672200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:29655600-29658400	Strong transcription	Aorta	Aorta
30	chr12:29655600-29659800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:29655600-29662200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:29655800-29657400	Weak transcription	Adipose Nuclei	Adipose
33	chr12:29656000-29659400	Weak transcription	Hela-S3	cervix
34	chr12:29656200-29657600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:29656200-29669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:29656200-29673800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:29656400-29666800	Weak transcription	Brain Substantia Nigra	brain
38	chr12:29656600-29660400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:29656800-29658400	Strong transcription	Left Ventricle	heart
40	chr12:29656800-29660000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:29657000-29666600	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:29657200-29675600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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