Variant report

Variant	rs10846524
Chromosome Location	chr12:123835521-123835522
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123832815..123836496-chr12:123847723..123851604,4	MCF-7	breast:
2	chr12:123833002..123837136-chr12:123847313..123849620,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256092	Chromatin interaction
ENSG00000139697	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10444447	0.82[ASN][1000 genomes]
rs10444448	0.82[ASN][1000 genomes]
rs10773007	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773009	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773010	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846495	0.82[ASN][1000 genomes]
rs10846496	0.82[ASN][1000 genomes]
rs10846498	0.82[ASN][1000 genomes]
rs10846499	0.82[ASN][1000 genomes]
rs10846500	0.82[ASN][1000 genomes]
rs10846501	0.82[ASN][1000 genomes]
rs10846503	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846504	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10846509	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10846510	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846511	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846514	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846518	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846521	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846522	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057231	0.82[ASN][1000 genomes]
rs11057240	0.82[ASN][1000 genomes]
rs11057243	0.91[ASN][1000 genomes]
rs11057250	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11057264	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057266	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057285	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057286	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371973	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376696	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28377694	1.00[ASN][1000 genomes]
rs28397122	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454135	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475177	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573826	1.00[ASN][1000 genomes]
rs28633324	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28646185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28655516	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28861152	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898283	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281511	0.91[ASN][1000 genomes]
rs4313613	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61953413	0.82[ASN][1000 genomes]
rs61955088	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61955089	0.91[ASN][1000 genomes]
rs61955114	0.91[ASN][1000 genomes]
rs61955117	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6488868	1.00[ASN][1000 genomes]
rs73231946	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10846524	CDK2AP1	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123773200-123838000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123773400-123837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:123773800-123837200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:123773800-123837400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:123807600-123845200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:123813800-123835600	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:123815200-123835600	Strong transcription	Fetal Intestine Small	intestine
9	chr12:123815200-123837200	Strong transcription	Fetal Stomach	stomach
10	chr12:123815600-123842000	Weak transcription	Psoas Muscle	Psoas
11	chr12:123816000-123838400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
13	chr12:123820400-123847000	Weak transcription	Fetal Brain Male	brain
14	chr12:123821600-123835600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:123827800-123835600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:123829000-123839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:123829000-123847400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:123829400-123840200	Weak transcription	Ovary	ovary
19	chr12:123830000-123835600	Weak transcription	Gastric	stomach
20	chr12:123830000-123837600	Weak transcription	HMEC	breast
21	chr12:123830000-123847400	Weak transcription	Brain Substantia Nigra	brain
22	chr12:123830000-123847400	Weak transcription	Colonic Mucosa	Colon
23	chr12:123830000-123847400	Weak transcription	NHLF	lung
24	chr12:123830200-123842200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:123830200-123847400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:123830200-123847400	Weak transcription	NHDF-Ad	bronchial
27	chr12:123830200-123847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:123830400-123838000	Weak transcription	Fetal Heart	heart
29	chr12:123830400-123840200	Weak transcription	HUVEC	blood vessel
30	chr12:123830400-123840600	Weak transcription	Small Intestine	intestine
31	chr12:123830400-123847600	Weak transcription	Aorta	Aorta
32	chr12:123830600-123847600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:123830800-123836600	Weak transcription	HSMM	muscle
34	chr12:123830800-123837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:123830800-123837600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:123830800-123837800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:123830800-123840200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:123830800-123844800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:123830800-123846600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:123830800-123847200	Weak transcription	Hela-S3	cervix
41	chr12:123830800-123847200	Weak transcription	HSMMtube	muscle
42	chr12:123832200-123837400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:123832400-123848200	Weak transcription	Esophagus	oesophagus
44	chr12:123832600-123840200	Weak transcription	Lung	lung
45	chr12:123832600-123840200	Weak transcription	Pancreas	Pancrea
46	chr12:123832600-123840400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:123832600-123846400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:123832600-123846600	Weak transcription	Spleen	Spleen
49	chr12:123832800-123836200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:123832800-123837800	Weak transcription	Primary T cells from cord blood	blood

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