Variant report

Variant	rs1239403
Chromosome Location	chr12:32439815-32439816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32433812..32435495-chr12:32439244..32441498,2	MCF-7	breast:
2	chr12:32429617..32432029-chr12:32437705..32440529,2	K562	blood:
3	chr12:32424959..32427093-chr12:32439775..32442095,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1151037	0.83[ASN][1000 genomes]
rs1239385	0.84[EUR][1000 genomes]
rs1239386	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1239400	0.84[EUR][1000 genomes]
rs1239573	0.84[EUR][1000 genomes]
rs1239574	0.84[EUR][1000 genomes]
rs1239576	0.88[ASN][1000 genomes]
rs1239577	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1239578	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1239579	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1239581	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1239582	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1239604	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs161977	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs184469	0.87[EUR][1000 genomes]
rs190511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2261339	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2261943	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442063	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2608396	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2608397	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2728802	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1239403	BICD1	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32426600-32443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:32426800-32442800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:32426800-32443200	Weak transcription	NH-A	brain
4	chr12:32426800-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:32427000-32443400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:32427000-32458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:32427000-32459400	Weak transcription	Aorta	Aorta
8	chr12:32427000-32463000	Weak transcription	NHLF	lung
9	chr12:32427200-32463000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:32427400-32445200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:32427600-32454400	Weak transcription	Primary B cells from cord blood	blood
12	chr12:32434800-32443000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:32435200-32448200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:32436200-32440200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:32436400-32440600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:32437200-32440000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:32437400-32440000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:32438000-32442800	Weak transcription	Osteobl	bone
19	chr12:32438200-32443200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:32438200-32443200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:32438200-32443200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:32438200-32449600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:32438800-32443200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:32438800-32443400	Weak transcription	Ovary	ovary
25	chr12:32438800-32449600	Weak transcription	Fetal Brain Female	brain
26	chr12:32439000-32440200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:32439000-32440200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:32439600-32443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:32439800-32443200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:32439800-32447000	Weak transcription	H1 Cell Line	embryonic stem cell

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