Variant report

Variant	rs17588963
Chromosome Location	chr12:32379810-32379811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1239596	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs161974	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs261882	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326639	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
rs17588963	BICD1	cis	Thyroid	GTEx

Chromatin state (count:76 , 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	chr12:32364800-32388000	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:32365000-32390000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:32365000-32390200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:32365200-32382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:32365600-32391200	Weak transcription	Fetal Brain Male	brain
7	chr12:32368400-32382800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:32369200-32380400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
10	chr12:32371000-32380800	Weak transcription	HSMM	muscle
11	chr12:32371000-32383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:32371000-32386000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:32371000-32389800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:32371000-32390000	Weak transcription	HSMMtube	muscle
15	chr12:32371000-32390200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:32371200-32380200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:32371200-32381000	Weak transcription	Lung	lung
18	chr12:32371200-32381600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:32371200-32382600	Weak transcription	HUVEC	blood vessel
20	chr12:32371200-32383000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:32371200-32383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:32371200-32390000	Weak transcription	Aorta	Aorta
23	chr12:32371200-32390000	Weak transcription	Brain Germinal Matrix	brain
24	chr12:32371200-32390000	Weak transcription	Fetal Muscle Leg	muscle
25	chr12:32371200-32390000	Weak transcription	Left Ventricle	heart
26	chr12:32371200-32390000	Weak transcription	Thymus	Thymus
27	chr12:32371200-32390200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:32371200-32393200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:32371200-32393400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:32371200-32406800	Weak transcription	Primary T cells from cord blood	blood
31	chr12:32371400-32381400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:32371400-32382600	Weak transcription	Fetal Thymus	thymus
33	chr12:32371600-32381400	Weak transcription	Fetal Intestine Large	intestine
34	chr12:32371600-32382400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:32371600-32383600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:32371600-32383800	Weak transcription	Fetal Brain Female	brain
37	chr12:32371600-32389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:32371600-32389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:32371600-32390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:32371600-32390000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:32371600-32390000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:32371600-32393000	Weak transcription	NH-A	brain
43	chr12:32371600-32393400	Weak transcription	NHDF-Ad	bronchial
44	chr12:32372000-32389400	Weak transcription	A549	lung
45	chr12:32372200-32389600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:32372400-32380200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:32374600-32380000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:32375400-32381000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:32375600-32380400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:32375800-32387600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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