Variant report

Variant	rs2016251
Chromosome Location	chr1:155914988-155914989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155879898..155882828-chr1:155912815..155915153,2	MCF-7	breast:
2	chr1:155913474..155915480-chr1:155951896..155954418,2	K562	blood:
3	chr1:155912393..155915782-chr1:156029437..156032638,3	K562	blood:
4	chr1:155910551..155912594-chr1:155912958..155915811,2	MCF-7	breast:
5	chr1:155912864..155915466-chr1:155921161..155923188,2	MCF-7	breast:
6	chr1:155887193..155889679-chr1:155914612..155916279,2	K562	blood:
7	chr1:155914514..155917947-chr1:155920172..155923593,3	MCF-7	breast:
8	chr1:155901960..155906403-chr1:155912698..155918499,7	MCF-7	breast:
9	chr1:155909425..155917901-chr1:155919093..155927049,14	K562	blood:
10	chr1:155913216..155915382-chr1:155955239..155957209,2	K562	blood:
11	chr1:155902449..155905054-chr1:155910368..155915421,5	MCF-7	breast:
12	chr1:155911219..155915431-chr1:155946632..155949866,4	MCF-7	breast:
13	chr1:155902078..155904595-chr1:155913787..155915362,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000132680	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000132698	Chromatin interaction
ENSG00000173080	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10796955	0.95[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes]
rs10908483	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1111102	0.81[CEU][hapmap]
rs11264426	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs11585845	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs12026057	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12037177	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12080846	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12091273	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12091361	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12118795	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs12144175	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12568523	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1889532	0.95[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes]
rs1889533	0.93[AMR][1000 genomes]
rs2282301	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2297649	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2364403	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3820594	0.91[MEX][hapmap]
rs4661218	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs66466805	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66669006	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6667652	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6670477	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6670493	0.95[CEU][hapmap]
rs6696019	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72708205	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7528441	0.80[AMR][1000 genomes]
rs7534858	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs7545308	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs867548	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs867549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs867550	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs915178	0.81[CEU][hapmap]
rs915181	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928596	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]

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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2016251	YY1AP1	cis	cerebellum	SCAN
rs2016251	HAPLN2	cis	parietal	SCAN
rs2016251	ADAM15	cis	multi-tissue	Pritchard
rs2016251	RIT1	cis	cerebellum	SCAN
rs2016251	SPRR3	cis	parietal	SCAN
rs2016251	PRUNE	cis	cerebellum	SCAN
rs2016251	ROBLD3	cis	parietal	SCAN
rs2016251	RIT1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155915200	Weak transcription	Fetal Brain Female	brain
2	chr1:155905000-155915800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:155905000-155915800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:155905000-155916000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:155905000-155916200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:155905400-155915800	Weak transcription	Thymus	Thymus
8	chr1:155905400-155918400	Weak transcription	Psoas Muscle	Psoas
9	chr1:155908000-155915800	Enhancers	Primary B cells from cord blood	blood
10	chr1:155908000-155915800	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:155908800-155916000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:155909400-155916000	Enhancers	Adipose Nuclei	Adipose
13	chr1:155909600-155916200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:155909600-155916400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:155909800-155916000	Enhancers	Fetal Intestine Large	intestine
16	chr1:155909800-155916200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:155910000-155915400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:155910600-155916000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:155910600-155917200	Weak transcription	Aorta	Aorta
20	chr1:155910800-155916000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:155911000-155915200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:155911400-155915800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:155911400-155916000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:155911600-155915800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:155911600-155915800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:155911600-155915800	Weak transcription	Osteobl	bone
28	chr1:155911600-155916200	Weak transcription	K562	blood
29	chr1:155911600-155916200	Weak transcription	NHDF-Ad	bronchial
30	chr1:155911800-155915000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:155911800-155915800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:155911800-155915800	Weak transcription	HSMMtube	muscle
33	chr1:155912000-155915000	Weak transcription	NH-A	brain
34	chr1:155912000-155915800	Weak transcription	Dnd41	blood
35	chr1:155912000-155916000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:155912000-155916200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:155912200-155918200	Weak transcription	Ovary	ovary
38	chr1:155912400-155916000	Weak transcription	HUVEC	blood vessel
39	chr1:155912400-155916600	Genic enhancers	Fetal Intestine Small	intestine
40	chr1:155912600-155916000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:155913000-155916000	Weak transcription	NHEK	skin
42	chr1:155913000-155916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:155913200-155915800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:155913200-155915800	Weak transcription	Left Ventricle	heart
45	chr1:155913200-155916000	Weak transcription	Esophagus	oesophagus
46	chr1:155913200-155916200	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:155913200-155916200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:155913200-155917800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:155913400-155915600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:155913600-155915800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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