Variant report

Variant	rs1239401
Chromosome Location	chr12:32407184-32407185
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32404264..32406924-chr12:32407131..32410038,2	K562	blood:
2	chr12:32406704..32407360-chr8:24560587..24561087,2	MCF-7	breast:
3	chr12:32359581..32362497-chr12:32406536..32409461,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1151038	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1151039	0.91[EUR][1000 genomes]
rs1239398	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]
rs1239399	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs155201	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs161979	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs161980	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs161981	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs185487	0.90[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2129590	0.90[CHB][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2608402	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2608403	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs261868	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs261869	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs261870	0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs261871	0.81[YRI][hapmap]
rs261877	0.81[YRI][hapmap]
rs2632344	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2632359	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs2632365	1.00[CHB][hapmap];0.80[GIH][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650125	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2728800	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2728801	0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs326633	0.92[ASW][hapmap];0.89[CHB][hapmap];1.00[LWK][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs326634	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs326636	0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs326637	0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs792474	0.85[CHB][hapmap]
rs792853	1.00[LWK][hapmap];0.93[YRI][hapmap]
rs792861	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs792863	0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs792866	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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
rs1239401	BICD1	cis	Thyroid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
2	chr12:32390800-32410600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:32391200-32408000	Weak transcription	Fetal Brain Female	brain
4	chr12:32391200-32409200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:32391600-32408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:32393600-32410400	Weak transcription	NHLF	lung
7	chr12:32393600-32423800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:32394000-32424200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:32394400-32423800	Weak transcription	NH-A	brain
10	chr12:32394600-32414400	Weak transcription	HUVEC	blood vessel
11	chr12:32401600-32410400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:32401800-32409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:32402000-32408400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:32402000-32409400	Weak transcription	Aorta	Aorta
15	chr12:32402000-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:32402000-32424000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:32402400-32423600	Weak transcription	Osteobl	bone
18	chr12:32403000-32417800	Weak transcription	Brain Angular Gyrus	brain
19	chr12:32403000-32417800	Weak transcription	Fetal Stomach	stomach
20	chr12:32403000-32424400	Weak transcription	HSMMtube	muscle
21	chr12:32403200-32407200	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:32403200-32407200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:32403200-32410800	Weak transcription	NHEK	skin
24	chr12:32403200-32411800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:32403200-32413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:32403200-32417600	Weak transcription	NHDF-Ad	bronchial
27	chr12:32403200-32424000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:32403200-32424400	Weak transcription	HSMM	muscle
29	chr12:32403400-32408000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:32403400-32411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:32403400-32413800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:32403400-32423600	Weak transcription	Brain Germinal Matrix	brain
33	chr12:32403800-32414400	Weak transcription	HMEC	breast
34	chr12:32404000-32407600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:32404600-32411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:32405000-32423800	Weak transcription	Left Ventricle	heart
37	chr12:32405400-32407400	Strong transcription	Dnd41	blood
38	chr12:32405400-32410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:32405400-32414200	Weak transcription	Spleen	Spleen
40	chr12:32405400-32417800	Weak transcription	Thymus	Thymus
41	chr12:32405600-32408000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:32405600-32423200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:32405600-32423800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:32405800-32413200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:32406000-32409200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:32406000-32418000	Weak transcription	Ovary	ovary
47	chr12:32406200-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:32406400-32407200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:32406400-32408800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:32406400-32409200	Weak transcription	A549	lung

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