Variant report

Variant	rs17012898
Chromosome Location	chr2:33601649-33601650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33591629..33594068-chr2:33601379..33603892,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13404913	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17012857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs17012892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17012924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17585007	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1804505	1.00[ASN][1000 genomes]
rs1869450	1.00[CHB][hapmap]
rs7589035	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7605700	1.00[ASN][1000 genomes]

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	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs17012898	UBXN2A	trans	brain	seeQTL
rs17012898	TM4SF1	trans	brain	seeQTL
rs17012898	C14orf126	trans	brain	seeQTL
rs17012898	CCDC82	trans	brain	seeQTL
rs17012898	SIPA1L3	trans	brain	seeQTL
rs17012898	USH1G	trans	brain	seeQTL
rs17012898	RNF11	trans	brain	seeQTL
rs17012898	OLIG3	trans	brain	seeQTL
rs17012898	MLLT1	trans	brain	seeQTL
rs17012898	NIPSNAP3A	trans	brain	seeQTL
rs17012898	IDO2	trans	brain	seeQTL
rs17012898	HIST1H4D	trans	brain	seeQTL
rs17012898	SLC16A1	trans	brain	seeQTL
rs17012898	TNIP3	trans	brain	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33529800-33609400	Weak transcription	Right Ventricle	heart
2	chr2:33578800-33612200	Weak transcription	Fetal Kidney	kidney
3	chr2:33581400-33602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:33581600-33611400	Weak transcription	Fetal Stomach	stomach
5	chr2:33582800-33601800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:33586200-33603600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:33588400-33624400	Weak transcription	Gastric	stomach
8	chr2:33589200-33623000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:33590600-33615800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:33590600-33624800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:33590800-33612600	Weak transcription	Ovary	ovary
12	chr2:33591400-33616000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:33591800-33601800	Weak transcription	NHLF	lung
14	chr2:33592000-33624800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:33595200-33609200	Weak transcription	Left Ventricle	heart
16	chr2:33596200-33614400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:33596400-33613800	Weak transcription	Liver	Liver
18	chr2:33596600-33603800	Weak transcription	NH-A	brain
19	chr2:33597000-33609000	Weak transcription	Fetal Heart	heart
20	chr2:33597200-33622200	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:33597400-33603600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:33597400-33610200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:33598000-33603800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:33598200-33605000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:33600400-33602000	Weak transcription	HSMMtube	muscle
26	chr2:33600600-33601800	Weak transcription	Osteobl	bone
27	chr2:33600600-33603400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:33600600-33603600	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:33600600-33603600	Weak transcription	Brain Substantia Nigra	brain
30	chr2:33600600-33603800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:33600600-33604000	Weak transcription	Adipose Nuclei	Adipose
32	chr2:33601200-33602600	Enhancers	NHDF-Ad	bronchial
33	chr2:33601400-33602200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:33601400-33602400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:33601400-33602600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:33601400-33602800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:33601400-33603000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:33601400-33603000	Enhancers	Aorta	Aorta
39	chr2:33601400-33603200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:33601600-33601800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:33601600-33602400	Strong transcription	HUVEC	blood vessel
42	chr2:33601600-33602600	Enhancers	HSMM	muscle
43	chr2:33601600-33602800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:33601600-33603200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:33601600-33604800	Enhancers	Cortex derived primary cultured neurospheres	brain

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