Variant report

Variant	rs17040543
Chromosome Location	chr4:110495858-110495859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110343481..110344216-chr4:110495251..110496139,3	K562	blood:
2	chr4:110348791..110349300-chr4:110495675..110496212,2	MCF-7	breast:
3	chr4:110480002..110482808-chr4:110493140..110496581,4	MCF-7	breast:
4	chr4:110495138..110497220-chr4:110499301..110501680,2	K562	blood:
5	chr4:110348797..110349339-chr4:110495526..110496188,3	MCF-7	breast:
6	chr4:110353379..110355385-chr4:110493462..110495883,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138802	Chromatin interaction
ENSG00000005059	Chromatin interaction
ENSG00000247950	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10213562	0.81[CEU][hapmap];0.85[MEX][hapmap]
rs11929713	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs11941206	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13142698	0.85[JPT][hapmap]
rs17040528	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6821382	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6821729	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687245	1.00[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9985964	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17040543	CAMK2D	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110483000-110498200	Weak transcription	HMEC	breast
2	chr4:110484000-110496000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:110484200-110509400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:110484400-110497200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:110484400-110509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:110484400-110509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:110484400-110509400	Weak transcription	Thymus	Thymus
8	chr4:110490000-110502600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:110493200-110497600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:110493800-110496000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:110494200-110496600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr4:110494400-110496000	Enhancers	Esophagus	oesophagus
13	chr4:110494600-110496400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:110494600-110498000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:110494800-110499600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr4:110495000-110498200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:110495200-110496000	Enhancers	Primary T cells from cord blood	blood
18	chr4:110495200-110496400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:110495200-110496400	Enhancers	Placenta	Placenta
20	chr4:110495200-110497200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:110495400-110496000	Enhancers	Stomach Mucosa	stomach
22	chr4:110495400-110496400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:110495400-110496600	Enhancers	Primary B cells from peripheral blood	blood
24	chr4:110495400-110496800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:110495400-110497200	Enhancers	Brain Germinal Matrix	brain
26	chr4:110495400-110497200	Enhancers	HUVEC	blood vessel
27	chr4:110495400-110498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:110495600-110496200	Enhancers	Dnd41	blood
29	chr4:110495800-110496000	Enhancers	Fetal Brain Male	brain
30	chr4:110495800-110496000	Enhancers	GM12878-XiMat	blood
31	chr4:110495800-110496200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr4:110495800-110496200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr4:110495800-110496400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr4:110495800-110496400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:110495800-110496400	Enhancers	Fetal Thymus	thymus
36	chr4:110495800-110498000	Enhancers	K562	blood

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