Variant report

Variant	rs2074995
Chromosome Location	chr17:16220491-16220492
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	chr17:16220122..16222963-chr17:16255326..16257269,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CENPV-1	chr17:16220016-16221006	ENSG00000250690

Variant related genes	Relation type
ENSG00000166582	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11655906	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11655907	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12449629	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12947973	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12948244	0.81[CEU][hapmap]
rs12948680	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12949255	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12949537	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2014604	0.88[CEU][hapmap]
rs28516015	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28862997	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3095171	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3112511	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112513	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3112521	0.87[CHB][hapmap]
rs3112524	0.87[CHB][hapmap]
rs3112526	0.87[CHB][hapmap]
rs3112527	0.87[CHB][hapmap]
rs3785621	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs3785623	0.88[CEU][hapmap]
rs4791665	0.88[CEU][hapmap]
rs4792735	0.82[EUR][1000 genomes]
rs6502499	0.86[CEU][hapmap]
rs7219687	0.88[CEU][hapmap]
rs7224367	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs917609	0.87[CHB][hapmap]
rs9890539	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9893005	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS 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	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2074995	ADORA2B	cis	Artery Tibial	GTEx
rs2074995	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs2074995	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs2074995	ADORA2B	cis	Muscle Skeletal	GTEx
rs2074995	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs2074995	ZSWIM7	cis	Muscle Skeletal	GTEx
rs2074995	CENPV	cis	Temporal Cortex	GTEx
rs2074995	CENPV	cis	Brain Pons	GTEx
rs2074995	CENPV	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16190600-16229600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:16190800-16220800	Weak transcription	Aorta	Aorta
3	chr17:16191400-16226000	Weak transcription	HSMMtube	muscle
4	chr17:16192800-16229000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr17:16197800-16230000	Weak transcription	Brain Angular Gyrus	brain
6	chr17:16200800-16228200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:16201000-16232400	Weak transcription	Hela-S3	cervix
8	chr17:16201200-16223200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:16201600-16228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
11	chr17:16201800-16221000	Weak transcription	Colonic Mucosa	Colon
12	chr17:16203600-16228800	Weak transcription	Primary B cells from cord blood	blood
13	chr17:16204200-16228800	Weak transcription	Brain Substantia Nigra	brain
14	chr17:16204600-16226000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:16205400-16228800	Weak transcription	Colon Smooth Muscle	Colon
16	chr17:16205800-16220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:16205800-16226000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr17:16205800-16228800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr17:16205800-16228800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:16205800-16229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:16205800-16229000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:16206000-16232200	Weak transcription	HMEC	breast
24	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
25	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:16206200-16228800	Weak transcription	Esophagus	oesophagus
27	chr17:16207400-16232400	Weak transcription	Right Atrium	heart
28	chr17:16208000-16221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:16214400-16228200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:16214400-16228600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr17:16214600-16220600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr17:16214600-16225800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:16214600-16228800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:16214600-16229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:16214600-16233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:16215800-16228800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:16216400-16222000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr17:16216400-16223400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr17:16216400-16231000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr17:16216600-16220800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr17:16216600-16221200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr17:16216600-16221400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr17:16216600-16221400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:16216800-16221000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:16216800-16221200	Strong transcription	Adipose Nuclei	Adipose
48	chr17:16216800-16223400	Strong transcription	Fetal Muscle Leg	muscle
49	chr17:16216800-16228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:16216800-16228800	Weak transcription	GM12878-XiMat	blood

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