Variant report

Variant	rs2341648
Chromosome Location	chr16:46985375-46985376
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	chr16:46983481..46986471-chr16:46987996..46989617,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10459877	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11247542	0.94[EUR][1000 genomes]
rs11247543	0.81[EUR][1000 genomes]
rs11859515	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12445492	0.92[EUR][1000 genomes]
rs12447719	0.94[EUR][1000 genomes]
rs12596824	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12719759	0.88[EUR][1000 genomes]
rs12925296	0.94[EUR][1000 genomes]
rs1362406	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1551188	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1894886	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1978336	0.94[EUR][1000 genomes]
rs2058673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35405784	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4577108	0.94[EUR][1000 genomes]
rs4625742	0.86[EUR][1000 genomes]
rs4966781	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966794	0.97[EUR][1000 genomes]
rs4966795	0.97[EUR][1000 genomes]
rs4966800	0.94[EUR][1000 genomes]
rs4967664	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4967696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4967724	0.81[EUR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967739	0.92[EUR][1000 genomes]
rs7189628	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7199379	0.94[EUR][1000 genomes]
rs7199772	0.97[EUR][1000 genomes]
rs7202325	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7203206	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8046142	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8047353	0.94[EUR][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8054039	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8058144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8058714	0.80[EUR][1000 genomes]
rs8060193	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9745921	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9923192	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925290	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925525	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9927843	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][hapmap]

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	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2341648	LOC388272	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46961800-46988600	Weak transcription	Hela-S3	cervix
2	chr16:46964200-46990600	Weak transcription	Spleen	Spleen
3	chr16:46964200-46991800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr16:46964600-46988600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:46964800-46988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr16:46965000-46990600	Weak transcription	Esophagus	oesophagus
7	chr16:46965200-46988000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr16:46965200-46990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr16:46965400-46988000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:46965400-46988600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr16:46965400-46988600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr16:46966000-46988800	Weak transcription	Fetal Brain Female	brain
13	chr16:46970400-46999000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:46977400-46988000	Weak transcription	Primary T cells from cord blood	blood
15	chr16:46977400-46988000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:46977400-46990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr16:46977400-46990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr16:46977600-46988000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr16:46977600-46988000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr16:46977600-46988000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr16:46977600-46988000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:46977600-46988200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:46977600-46988400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr16:46977600-46988400	Weak transcription	Placenta	Placenta
25	chr16:46977600-46988600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr16:46977600-46991000	Weak transcription	Lung	lung
27	chr16:46977600-47006200	Weak transcription	Stomach Mucosa	stomach
28	chr16:46977800-46988400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:46979800-46990600	Weak transcription	Gastric	stomach
30	chr16:46980200-46988200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr16:46980200-46990600	Weak transcription	Pancreas	Pancrea
32	chr16:46981800-46988000	Weak transcription	Brain Germinal Matrix	brain
33	chr16:46981800-46988800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr16:46982200-46990000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr16:46982200-46990600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr16:46982800-46988600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr16:46982800-46990800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr16:46983000-46988400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr16:46983400-46988600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr16:46983400-46990000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr16:46983400-46990600	Weak transcription	Psoas Muscle	Psoas
42	chr16:46983400-46990800	Weak transcription	Right Ventricle	heart
43	chr16:46983600-46988000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr16:46983800-46988000	Weak transcription	GM12878-XiMat	blood
45	chr16:46983800-46988600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:46983800-46996200	Weak transcription	Small Intestine	intestine
47	chr16:46984200-46987600	Weak transcription	Liver	Liver
48	chr16:46984200-46988000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr16:46984200-46988000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr16:46984400-46987400	Weak transcription	Duodenum Mucosa	Duodenum

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