Variant report

Variant	rs2288486
Chromosome Location	chr16:71513034-71513035
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71492243..71500079-chr16:71512817..71521299,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167377	Chromatin interaction
ENSG00000247324	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10500558	0.95[ASN][1000 genomes]
rs11640165	0.95[ASN][1000 genomes]
rs11641492	0.95[ASN][1000 genomes]
rs11643101	0.82[JPT][hapmap]
rs11643216	0.95[ASN][1000 genomes]
rs11644434	0.84[JPT][hapmap]
rs11647749	0.94[ASN][1000 genomes]
rs12446461	0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs13331346	0.98[ASN][1000 genomes]
rs1609868	0.82[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1609869	0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2004672	0.93[ASN][1000 genomes]
rs2070832	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs2288487	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2288488	1.00[ASN][1000 genomes]
rs2303788	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2432524	0.82[CHB][hapmap]
rs28372238	0.93[ASN][1000 genomes]
rs310334	0.83[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs35373081	0.97[ASN][1000 genomes]
rs35916432	0.88[ASN][1000 genomes]
rs36063092	0.84[ASN][1000 genomes]
rs3813743	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4149498	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4503795	0.94[ASN][1000 genomes]
rs4620964	0.82[ASN][1000 genomes]
rs58134724	0.98[ASN][1000 genomes]
rs58452291	0.83[ASN][1000 genomes]
rs58719913	0.95[ASN][1000 genomes]
rs6499523	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7184543	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7186241	0.94[ASN][1000 genomes]
rs7187165	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7187354	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs7188342	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7199026	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7199373	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7200335	0.91[ASN][1000 genomes]
rs7200431	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7202662	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7202953	0.95[ASN][1000 genomes]
rs730470	0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs732318	0.82[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs74026831	0.94[ASN][1000 genomes]
rs74027246	0.95[ASN][1000 genomes]
rs8044068	0.93[ASN][1000 genomes]
rs8044561	0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs8051212	0.88[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs8053662	0.93[ASN][1000 genomes]
rs8058294	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8058776	0.87[ASN][1000 genomes]
rs8061078	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs9302623	0.96[ASN][1000 genomes]
rs9926110	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs9928243	0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9933680	0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9935426	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9936249	0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs9940771	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2288486	HYDIN	cis	parietal	SCAN
rs2288486	RANBP10	cis	parietal	SCAN
rs2288486	CHTF8	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
3	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:71502800-71517400	Weak transcription	Dnd41	blood
5	chr16:71504600-71513600	Strong transcription	Stomach Smooth Muscle	stomach
6	chr16:71506400-71517400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:71507200-71514800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr16:71507200-71517800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:71507400-71517800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr16:71507600-71517400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr16:71507600-71517400	Weak transcription	Fetal Brain Male	brain
12	chr16:71507800-71513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:71508400-71517600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr16:71508400-71517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr16:71508800-71517800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr16:71509600-71517600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:71509800-71517800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:71509800-71517800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:71510000-71517600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr16:71510000-71517800	Weak transcription	Esophagus	oesophagus
21	chr16:71510200-71517600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr16:71510200-71518000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:71510600-71517600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:71510600-71517600	Weak transcription	NHEK	skin
25	chr16:71510600-71517800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr16:71510600-71518000	Weak transcription	Gastric	stomach
27	chr16:71510800-71517400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr16:71510800-71517600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr16:71510800-71518000	Weak transcription	Small Intestine	intestine
30	chr16:71511000-71514000	Weak transcription	HSMMtube	muscle
31	chr16:71511000-71517400	Weak transcription	NHDF-Ad	bronchial
32	chr16:71511200-71517600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:71511200-71517600	Weak transcription	HMEC	breast
34	chr16:71511200-71517800	Weak transcription	NH-A	brain
35	chr16:71511400-71513600	Weak transcription	K562	blood
36	chr16:71511400-71517800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr16:71511800-71517400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:71511800-71517400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr16:71511800-71517600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr16:71511800-71517600	Weak transcription	HUVEC	blood vessel
41	chr16:71512000-71517200	Weak transcription	GM12878-XiMat	blood
42	chr16:71512000-71517400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr16:71512000-71517400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr16:71512000-71517400	Weak transcription	Psoas Muscle	Psoas
45	chr16:71512200-71515400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr16:71512200-71517600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr16:71512200-71518000	Weak transcription	Placenta	Placenta
48	chr16:71512400-71517400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr16:71512400-71517400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:71512400-71517400	Weak transcription	A549	lung

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