Variant report

Variant	rs2052873
Chromosome Location	chr16:71505303-71505304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71490795..71493045-chr16:71503672..71506458,2	K562	blood:
2	chr16:71504965..71506764-chr16:71524563..71526143,2	K562	blood:
3	chr16:71504762..71507236-chr16:71509593..71512439,2	K562	blood:
4	chr16:71504129..71506148-chr16:71516935..71519923,2	MCF-7	breast:
5	chr16:71497700..71500390-chr16:71504714..71506907,2	K562	blood:
6	chr16:71492607..71498322-chr16:71498324..71506196,11	MCF-7	breast:
7	chr16:71493295..71494894-chr16:71504109..71506023,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157429	Chromatin interaction
ENSG00000167377	Chromatin interaction
ENSG00000247324	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10468265	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866859	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12325234	0.90[CEU][hapmap]
rs12444714	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs12918320	0.90[CEU][hapmap];1.00[TSI][hapmap]
rs12919092	0.90[CEU][hapmap]
rs13336809	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972266	1.00[ASN][1000 genomes]
rs16972805	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16972808	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973000	1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs16973112	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973190	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973286	0.90[EUR][1000 genomes]
rs1804984	0.96[EUR][1000 genomes]
rs3886947	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258624	1.00[JPT][hapmap]
rs56222754	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57821244	0.89[EUR][1000 genomes]
rs59364668	0.87[EUR][1000 genomes]
rs61171207	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499520	0.89[CEU][hapmap]
rs6499521	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7188021	1.00[ASN][1000 genomes]
rs7197127	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72791971	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72791974	0.97[EUR][1000 genomes]
rs72795864	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795867	0.86[EUR][1000 genomes]
rs72795869	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795881	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797728	0.90[EUR][1000 genomes]
rs8044168	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8049040	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8050135	1.00[ASN][1000 genomes]
rs8051439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056735	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940485	1.00[ASN][1000 genomes]
rs9989376	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9989377	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2052873	COG4	cis	parietal	SCAN
rs2052873	C16orf86	cis	parietal	SCAN
rs2052873	SNTB2	cis	cerebellum	SCAN
rs2052873	RANBP10	cis	parietal	SCAN
rs2052873	ZNF19	cis	cerebellum	SCAN
rs2052873	RP11-510M2.10	cis	Skin Sun Exposed Lower leg	GTEx
rs2052873	ZNF23	cis	parietal	SCAN
rs2052873	CMTM1	cis	cerebellum	SCAN
rs2052873	CTCF	cis	cerebellum	SCAN
rs2052873	CBFB	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71496400-71509400	Weak transcription	Small Intestine	intestine
2	chr16:71496600-71507600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:71496600-71508400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:71496600-71508400	Weak transcription	Placenta	Placenta
5	chr16:71496600-71509200	Weak transcription	Fetal Intestine Large	intestine
6	chr16:71496600-71509400	Weak transcription	Colonic Mucosa	Colon
7	chr16:71496600-71509400	Weak transcription	Esophagus	oesophagus
8	chr16:71496600-71509400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr16:71496600-71511400	Weak transcription	Pancreas	Pancrea
10	chr16:71496800-71507600	Weak transcription	Ovary	ovary
11	chr16:71496800-71507800	Weak transcription	Fetal Muscle Leg	muscle
12	chr16:71496800-71507800	Weak transcription	Left Ventricle	heart
13	chr16:71496800-71507800	Weak transcription	HSMM	muscle
14	chr16:71496800-71507800	Weak transcription	HSMMtube	muscle
15	chr16:71496800-71508400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:71496800-71508600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr16:71496800-71508600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:71496800-71508600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr16:71496800-71508800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr16:71496800-71508800	Weak transcription	Primary T cells from cord blood	blood
21	chr16:71496800-71508800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr16:71496800-71508800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr16:71496800-71508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr16:71496800-71509000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr16:71496800-71509200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr16:71496800-71509400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr16:71496800-71509400	Weak transcription	Psoas Muscle	Psoas
28	chr16:71496800-71512000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:71496800-71512200	Weak transcription	Fetal Intestine Small	intestine
30	chr16:71497000-71507800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:71497000-71507800	Weak transcription	NHLF	lung
32	chr16:71497000-71508000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr16:71497000-71508400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr16:71497000-71508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:71497000-71511800	Weak transcription	Brain Substantia Nigra	brain
36	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
38	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr16:71497200-71507800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr16:71497200-71508400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:71497200-71508600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:71497200-71508600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr16:71497200-71509000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr16:71497200-71509200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr16:71497200-71509400	Weak transcription	Colon Smooth Muscle	Colon
46	chr16:71497200-71509400	Weak transcription	Lung	lung
47	chr16:71497400-71508800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr16:71497400-71509000	Weak transcription	Right Ventricle	heart
49	chr16:71497400-71509200	Weak transcription	Primary B cells from cord blood	blood
50	chr16:71497400-71509200	Weak transcription	Brain Angular Gyrus	brain

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