Variant report

Variant	rs2608396
Chromosome Location	chr12:32406237-32406238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32404264..32406924-chr12:32407131..32410038,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1239400	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1239403	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1239577	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1239578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1239579	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1239581	0.90[EUR][1000 genomes]
rs1239582	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1239604	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs161974	0.83[YRI][hapmap]
rs161977	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs179104	0.85[CEU][hapmap]
rs184469	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs190511	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2261339	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2261943	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2442063	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2594009	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2594010	0.90[JPT][hapmap]
rs2608397	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632366	0.81[EUR][1000 genomes]
rs2650124	0.81[EUR][1000 genomes]
rs2650142	1.00[JPT][hapmap]
rs2650144	0.92[CHD][hapmap];0.90[JPT][hapmap]
rs2650145	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2728802	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326639	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs326640	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs326641	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs326643	0.85[CEU][hapmap]
rs326644	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs326645	0.85[CEU][hapmap]
rs326646	0.94[ASW][hapmap];0.85[CEU][hapmap];0.80[GIH][hapmap];0.97[LWK][hapmap];0.89[TSI][hapmap]
rs7314519	0.81[EUR][1000 genomes]
rs811078	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs812645	0.84[CEU][hapmap]

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
rs2608396	BICD1	cis	Thyroid	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32370200-32407800	Weak transcription	Hela-S3	cervix
2	chr12:32371200-32406800	Weak transcription	Primary T cells from cord blood	blood
3	chr12:32390800-32410600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:32391200-32408000	Weak transcription	Fetal Brain Female	brain
5	chr12:32391200-32409200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:32391600-32408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:32393600-32410400	Weak transcription	NHLF	lung
8	chr12:32393600-32423800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:32394000-32424200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr12:32394400-32423800	Weak transcription	NH-A	brain
11	chr12:32394600-32414400	Weak transcription	HUVEC	blood vessel
12	chr12:32401600-32410400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:32401800-32409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:32402000-32408400	Weak transcription	Fetal Intestine Small	intestine
15	chr12:32402000-32409400	Weak transcription	Aorta	Aorta
16	chr12:32402000-32417800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:32402000-32424000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:32402400-32423600	Weak transcription	Osteobl	bone
19	chr12:32403000-32417800	Weak transcription	Brain Angular Gyrus	brain
20	chr12:32403000-32417800	Weak transcription	Fetal Stomach	stomach
21	chr12:32403000-32424400	Weak transcription	HSMMtube	muscle
22	chr12:32403200-32406600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:32403200-32407200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:32403200-32407200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:32403200-32410800	Weak transcription	NHEK	skin
26	chr12:32403200-32411800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:32403200-32413400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:32403200-32417600	Weak transcription	NHDF-Ad	bronchial
29	chr12:32403200-32424000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:32403200-32424400	Weak transcription	HSMM	muscle
31	chr12:32403400-32406600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:32403400-32408000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:32403400-32411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:32403400-32413800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:32403400-32423600	Weak transcription	Brain Germinal Matrix	brain
36	chr12:32403800-32406800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:32403800-32414400	Weak transcription	HMEC	breast
38	chr12:32404000-32407600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:32404600-32406600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr12:32404600-32411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:32405000-32423800	Weak transcription	Left Ventricle	heart
42	chr12:32405400-32407400	Strong transcription	Dnd41	blood
43	chr12:32405400-32410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:32405400-32414200	Weak transcription	Spleen	Spleen
45	chr12:32405400-32417800	Weak transcription	Thymus	Thymus
46	chr12:32405600-32406400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:32405600-32406400	Enhancers	A549	lung
48	chr12:32405600-32407000	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr12:32405600-32408000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:32405600-32423200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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