Variant report

Variant	rs17884212
Chromosome Location	chr22:29141917-29141918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:
2	chr22:29140753..29143117-chr22:29145529..29147123,2	K562	blood:

Variant related genes	Relation type
ENSG00000272858	Chromatin interaction
ENSG00000226471	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17879734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17880353	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17880459	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17881056	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17883144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17885109	0.80[AFR][1000 genomes]
rs17885728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5762814	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs9620817	0.91[YRI][hapmap]

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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17884212	CHEK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29139000-29143200	Weak transcription	Small Intestine	intestine
2	chr22:29139000-29143400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:29139200-29144400	Weak transcription	Right Ventricle	heart
4	chr22:29139200-29146000	Weak transcription	Fetal Brain Male	brain
5	chr22:29139200-29153800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:29139400-29142800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr22:29139400-29143400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr22:29139400-29144200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr22:29139400-29145000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:29139400-29145600	Strong transcription	HSMM	muscle
11	chr22:29139400-29149400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr22:29139400-29156400	Weak transcription	Stomach Mucosa	stomach
13	chr22:29139600-29144000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr22:29139600-29144600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr22:29139600-29144600	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr22:29139600-29145800	Strong transcription	Fetal Thymus	thymus
17	chr22:29139600-29146400	Weak transcription	NHLF	lung
18	chr22:29139600-29146800	Strong transcription	Primary T cells from cord blood	blood
19	chr22:29139600-29148200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:29139600-29148600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr22:29139600-29149600	Weak transcription	K562	blood
22	chr22:29139800-29143000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:29139800-29143400	Weak transcription	NHEK	skin
24	chr22:29139800-29143600	Strong transcription	Thymus	Thymus
25	chr22:29139800-29143800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr22:29139800-29144200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr22:29139800-29144200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr22:29139800-29144200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:29139800-29144400	Strong transcription	Brain Hippocampus Middle	brain
30	chr22:29139800-29144400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr22:29139800-29144600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr22:29139800-29144600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr22:29139800-29144600	Strong transcription	Dnd41	blood
34	chr22:29139800-29144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:29139800-29145200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:29139800-29145200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:29139800-29145400	Strong transcription	Left Ventricle	heart
38	chr22:29139800-29145800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr22:29139800-29145800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr22:29139800-29146000	Strong transcription	Brain Anterior Caudate	brain
41	chr22:29139800-29146000	Strong transcription	Fetal Lung	lung
42	chr22:29139800-29146200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr22:29139800-29146600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr22:29139800-29146800	Strong transcription	Fetal Intestine Large	intestine
45	chr22:29139800-29147400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr22:29139800-29147400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr22:29139800-29147600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr22:29139800-29147800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr22:29139800-29147800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr22:29139800-29147800	Strong transcription	Lung	lung

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