Variant report

Variant	rs2288693
Chromosome Location	chr12:121687474-121687475
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	chr12:121673925..121677209-chr12:121686132..121689078,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11065570	1.00[YRI][hapmap]
rs1169721	0.88[CHB][hapmap]
rs1653586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1653592	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718118	0.86[EUR][1000 genomes]
rs1718156	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1718158	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071272	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2252298	1.00[EUR][1000 genomes]
rs2252304	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2288691	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs25642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2567982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668239	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686339	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28360477	1.00[YRI][hapmap]
rs28969487	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751145	1.00[AFR][1000 genomes]
rs3815990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57379013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57419819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57983015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59037892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60714133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60979871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv899564	chr12:121641509-121689798	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899565	chr12:121641509-121698785	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2288693	CAMKK2	cis	brain	seeQTL
rs2288693	CAMKK2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121653200-121698800	Weak transcription	Fetal Heart	heart
2	chr12:121662800-121690600	Weak transcription	Fetal Brain Male	brain
3	chr12:121670200-121689400	Strong transcription	Fetal Brain Female	brain
4	chr12:121670600-121695000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:121674400-121687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:121674600-121692800	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:121674600-121704200	Strong transcription	Brain Germinal Matrix	brain
8	chr12:121677400-121688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:121677400-121695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:121677400-121717000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:121677400-121717200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:121677600-121688400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:121678600-121690400	Weak transcription	Psoas Muscle	Psoas
14	chr12:121679000-121713000	Strong transcription	Fetal Intestine Large	intestine
15	chr12:121679200-121709200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:121679200-121714400	Weak transcription	Right Atrium	heart
17	chr12:121679400-121699000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:121679400-121713800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:121679600-121688400	Weak transcription	HSMM	muscle
20	chr12:121679600-121690800	Weak transcription	K562	blood
21	chr12:121679600-121708800	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:121679600-121709200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr12:121679600-121713000	Strong transcription	Liver	Liver
24	chr12:121679600-121732600	Strong transcription	Fetal Intestine Small	intestine
25	chr12:121679800-121687800	Weak transcription	NHDF-Ad	bronchial
26	chr12:121679800-121690400	Strong transcription	Fetal Stomach	stomach
27	chr12:121679800-121694600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:121679800-121703200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:121679800-121709000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:121679800-121713000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:121679800-121713600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:121680000-121709800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:121680200-121690600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:121680400-121690600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:121680800-121689000	Strong transcription	Right Ventricle	heart
36	chr12:121680800-121713800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:121681000-121689400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:121681000-121709000	Strong transcription	Adipose Nuclei	Adipose
39	chr12:121681000-121712600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:121681200-121687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:121681200-121689000	Strong transcription	Pancreas	Pancrea
42	chr12:121681200-121689600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:121681200-121693400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:121681200-121693800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:121681200-121706400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:121681200-121708800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:121681200-121708800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:121681200-121708800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:121681200-121713600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:121681200-121717800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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