Variant report

Variant	rs17046514
Chromosome Location	chr2:55185862-55185863
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	chr2:55184760..55187706-chr2:55190562..55193036,2	MCF-7	breast:
2	chr2:55183507..55185896-chr2:55194020..55195726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1012603	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10496034	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10496040	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11683784	0.84[GIH][hapmap]
rs12464877	1.00[ASW][hapmap]
rs17046518	0.84[EUR][1000 genomes]
rs17046583	0.82[CEU][hapmap];0.83[AFR][1000 genomes]
rs17046643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17046658	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2028728	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2241958	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2255026	0.83[AFR][1000 genomes]
rs2304687	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2580768	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs2580770	1.00[ASW][hapmap]
rs2580771	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs2588515	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs2588516	0.83[AFR][1000 genomes]
rs2588522	0.83[AFR][1000 genomes]
rs2919126	0.83[AFR][1000 genomes]
rs34378852	0.83[AFR][1000 genomes]
rs4233955	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671991	0.86[CHB][hapmap]
rs4671993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4671995	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671997	0.96[EUR][1000 genomes]
rs4672003	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs4672006	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4672009	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4672011	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4672018	1.00[ASW][hapmap]
rs57737203	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs60553807	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs60989687	0.81[EUR][1000 genomes]
rs61486548	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6545464	0.83[AFR][1000 genomes]
rs6734314	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs6739210	0.83[AFR][1000 genomes]
rs733916	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73936818	0.86[EUR][1000 genomes]
rs73936829	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17046514	LOC344405	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
4	chr2:55173200-55187000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55173200-55203400	Weak transcription	Gastric	stomach
6	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
8	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
9	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain
10	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:55177800-55193800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:55178200-55193400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55178600-55193400	Weak transcription	Spleen	Spleen
15	chr2:55180400-55189600	Weak transcription	HSMMtube	muscle
16	chr2:55180600-55191600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:55180600-55193600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:55180600-55195400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:55180600-55196000	Weak transcription	NH-A	brain
20	chr2:55180800-55191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:55181600-55193600	Weak transcription	Lung	lung
22	chr2:55181600-55203400	Weak transcription	Ovary	ovary
23	chr2:55182400-55186600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:55183000-55191600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:55183000-55191600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55183000-55192000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:55183200-55193200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55183200-55193200	Weak transcription	NHLF	lung
29	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
30	chr2:55183400-55196600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:55183800-55186600	Enhancers	K562	blood
32	chr2:55183800-55190400	Weak transcription	HepG2	liver
33	chr2:55183800-55190600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:55183800-55193600	Weak transcription	A549	lung
35	chr2:55184000-55189400	Weak transcription	Fetal Intestine Large	intestine
36	chr2:55184000-55189400	Weak transcription	Fetal Intestine Small	intestine
37	chr2:55184000-55192200	Weak transcription	Fetal Stomach	stomach
38	chr2:55184400-55186400	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:55184600-55188200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:55184800-55192400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:55184800-55195800	Weak transcription	Thymus	Thymus
42	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:55185000-55190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:55185000-55192800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:55185200-55191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:55185200-55191000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:55185200-55191000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:55185200-55193400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:55185200-55194000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:55185400-55187800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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