Variant report

Variant	rs2728800
Chromosome Location	chr12:32425616-32425617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32337947..32340107-chr12:32424491..32426226,2	MCF-7	breast:
2	chr12:32425311..32427428-chr12:32433944..32435788,2	K562	blood:
3	chr12:32424959..32427093-chr12:32439775..32442095,2	MCF-7	breast:
4	chr12:32418322..32421345-chr12:32425361..32428324,3	K562	blood:

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

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

rs_ID	r²[population]
rs1151038	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1151039	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151045	0.85[ASN][1000 genomes]
rs1239398	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1239401	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs155201	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161979	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161980	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161981	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs185487	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2129590	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2594000	0.85[ASN][1000 genomes]
rs261868	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261869	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs261870	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2632344	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632365	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2650125	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2650137	0.85[ASN][1000 genomes]
rs2728704	0.85[ASN][1000 genomes]
rs2728705	0.80[ASN][1000 genomes]
rs2728801	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs708225	0.85[ASN][1000 genomes]
rs708226	0.85[ASN][1000 genomes]
rs708227	0.85[ASN][1000 genomes]
rs751720	0.85[ASN][1000 genomes]
rs753296	0.85[ASN][1000 genomes]
rs792473	0.85[ASN][1000 genomes]
rs792474	0.93[ASN][1000 genomes]
rs792861	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs792863	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs792866	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs806784	0.85[ASN][1000 genomes]
rs814243	0.85[ASN][1000 genomes]
rs901598	0.85[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
rs2728800	BICD1	cis	Thyroid	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32411200-32426200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:32412600-32426000	Weak transcription	K562	blood
3	chr12:32413400-32437600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:32418400-32426400	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:32418600-32428400	Weak transcription	Ovary	ovary
6	chr12:32419200-32426600	Weak transcription	Dnd41	blood
7	chr12:32421000-32426000	Weak transcription	Pancreas	Pancrea
8	chr12:32421400-32426200	Weak transcription	Aorta	Aorta
9	chr12:32422200-32427400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:32423400-32427000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:32423600-32426000	Enhancers	Primary B cells from cord blood	blood
12	chr12:32423600-32427200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:32423600-32427200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:32423600-32427400	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:32423800-32427200	Enhancers	Fetal Intestine Large	intestine
16	chr12:32423800-32427800	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:32424000-32426200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:32424000-32426400	Enhancers	Rectal Smooth Muscle	rectum
19	chr12:32424000-32427000	Enhancers	Fetal Brain Female	brain
20	chr12:32424000-32427200	Enhancers	Fetal Intestine Small	intestine
21	chr12:32424200-32426000	Weak transcription	Spleen	Spleen
22	chr12:32424200-32426200	Weak transcription	Lung	lung
23	chr12:32424400-32426000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:32424400-32426000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:32424400-32426400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:32424400-32426400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:32424400-32426800	Weak transcription	Right Atrium	heart
28	chr12:32424400-32434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:32424600-32426000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:32424600-32426000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:32424600-32426000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:32424600-32426000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:32424600-32426000	Weak transcription	NHDF-Ad	bronchial
34	chr12:32424600-32426200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr12:32424600-32426200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:32424600-32426800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:32424600-32438000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:32424800-32425800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:32424800-32425800	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:32424800-32426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:32424800-32426000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:32424800-32426000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:32424800-32426000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:32424800-32426000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr12:32424800-32426000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:32424800-32426000	Weak transcription	Brain Angular Gyrus	brain
47	chr12:32424800-32426000	Weak transcription	Brain Anterior Caudate	brain
48	chr12:32424800-32426000	Weak transcription	Brain Substantia Nigra	brain
49	chr12:32424800-32426000	Weak transcription	Fetal Brain Male	brain
50	chr12:32424800-32426000	Weak transcription	NHLF	lung

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