Variant report

Variant	rs1239398
Chromosome Location	chr12:32411399-32411400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32111261..32114014-chr12:32410835..32414194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174718	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1151038	0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151039	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs1239399	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1239401	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155201	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161979	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161980	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161981	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs185487	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2129590	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2608402	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2608403	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs261868	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs261869	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs261870	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs261883	0.83[YRI][hapmap]
rs2632344	0.83[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2632359	0.86[CHB][hapmap];0.81[YRI][hapmap]
rs2632365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2650125	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2728800	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2728801	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs326633	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs326634	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs326636	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs326637	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs792474	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs792853	0.94[YRI][hapmap]
rs792861	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs792863	0.87[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs792866	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][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
rs1239398	BICD1	cis	Thyroid	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32393600-32423800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:32394000-32424200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:32394400-32423800	Weak transcription	NH-A	brain
4	chr12:32394600-32414400	Weak transcription	HUVEC	blood vessel
5	chr12:32402000-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:32402000-32424000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32402400-32423600	Weak transcription	Osteobl	bone
8	chr12:32403000-32417800	Weak transcription	Brain Angular Gyrus	brain
9	chr12:32403000-32417800	Weak transcription	Fetal Stomach	stomach
10	chr12:32403000-32424400	Weak transcription	HSMMtube	muscle
11	chr12:32403200-32411800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:32403200-32413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:32403200-32417600	Weak transcription	NHDF-Ad	bronchial
14	chr12:32403200-32424000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:32403200-32424400	Weak transcription	HSMM	muscle
16	chr12:32403400-32413800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:32403400-32423600	Weak transcription	Brain Germinal Matrix	brain
18	chr12:32403800-32414400	Weak transcription	HMEC	breast
19	chr12:32404600-32411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:32405000-32423800	Weak transcription	Left Ventricle	heart
21	chr12:32405400-32414200	Weak transcription	Spleen	Spleen
22	chr12:32405400-32417800	Weak transcription	Thymus	Thymus
23	chr12:32405600-32423200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:32405600-32423800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:32405800-32413200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:32406000-32418000	Weak transcription	Ovary	ovary
27	chr12:32406200-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:32406600-32417800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:32407000-32423600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:32407400-32417800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:32407800-32423400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:32408200-32424000	Weak transcription	Hela-S3	cervix
33	chr12:32408200-32425600	Weak transcription	Primary T cells from cord blood	blood
34	chr12:32408400-32413800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:32409400-32423600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr12:32409400-32423800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:32409600-32414600	Weak transcription	Fetal Thymus	thymus
38	chr12:32410400-32411600	ZNF genes & repeats	GM12878-XiMat	blood
39	chr12:32410600-32411600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr12:32411000-32411400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:32411000-32411600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:32411200-32411400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr12:32411200-32411400	Active TSS	K562	blood
44	chr12:32411200-32413200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:32411200-32413600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:32411200-32413600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:32411200-32413600	Weak transcription	NHEK	skin
48	chr12:32411200-32414200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:32411200-32414400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:32411200-32416600	Weak transcription	Primary B cells from cord blood	blood

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