Variant report

Variant	rs2650147
Chromosome Location	chr12:32382860-32382861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32378528..32381260-chr12:32382291..32384074,2	K562	blood:
2	chr12:32381480..32383173-chr12:32412418..32414240,2	MCF-7	breast:
3	chr12:32382555..32384109-chr12:32396611..32398955,2	K562	blood:
4	chr12:32375628..32378407-chr12:32382198..32383979,2	K562	blood:

Variant related genes	Relation type
ENSG00000258134	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2608402	0.81[AFR][1000 genomes]
rs2608403	0.82[AFR][1000 genomes]
rs261881	0.84[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs261883	0.83[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs261886	0.86[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs261887	0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs326633	0.81[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs326636	0.84[YRI][hapmap]
rs792853	0.83[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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
rs2650147	BICD1	cis	Thyroid	GTEx

Chromatin state (count:63 , 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	chr12:32365600-32391200	Weak transcription	Fetal Brain Male	brain
6	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
7	chr12:32371000-32383000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:32371000-32386000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:32371000-32389800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:32371000-32390000	Weak transcription	HSMMtube	muscle
11	chr12:32371000-32390200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:32371200-32383000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:32371200-32383000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:32371200-32390000	Weak transcription	Aorta	Aorta
15	chr12:32371200-32390000	Weak transcription	Brain Germinal Matrix	brain
16	chr12:32371200-32390000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:32371200-32390000	Weak transcription	Left Ventricle	heart
18	chr12:32371200-32390000	Weak transcription	Thymus	Thymus
19	chr12:32371200-32390200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:32371200-32393200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:32371200-32393400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:32371200-32406800	Weak transcription	Primary T cells from cord blood	blood
23	chr12:32371600-32383600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:32371600-32383800	Weak transcription	Fetal Brain Female	brain
25	chr12:32371600-32389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:32371600-32389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:32371600-32390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:32371600-32390000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:32371600-32390000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:32371600-32393000	Weak transcription	NH-A	brain
31	chr12:32371600-32393400	Weak transcription	NHDF-Ad	bronchial
32	chr12:32372000-32389400	Weak transcription	A549	lung
33	chr12:32372200-32389600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:32375800-32387600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:32377400-32390000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:32377400-32390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:32377600-32390200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:32379800-32385800	Weak transcription	Ovary	ovary
39	chr12:32380000-32387200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:32380000-32401000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:32380600-32389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:32380600-32390000	Weak transcription	Fetal Intestine Small	intestine
43	chr12:32380600-32393200	Weak transcription	Spleen	Spleen
44	chr12:32380800-32390200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:32381000-32389400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:32381000-32389400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:32381000-32389400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:32381000-32389400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:32381000-32389400	Weak transcription	Dnd41	blood
50	chr12:32381000-32390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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