Variant report

Variant	rs28416529
Chromosome Location	chr1:153595381-153595382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153541191..153544684-chr1:153594586..153597033,3	MCF-7	breast:
2	chr1:153539227..153541131-chr1:153594881..153597093,2	MCF-7	breast:
3	chr1:153527411..153530387-chr1:153595127..153597966,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1046381	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10797056	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10797090	0.82[EUR][1000 genomes]
rs10908746	0.85[EUR][1000 genomes]
rs1128894	0.85[EUR][1000 genomes]
rs11497739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11548102	0.96[ASN][1000 genomes]
rs11548103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580122	0.82[EUR][1000 genomes]
rs12564925	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs1411273	0.95[EUR][1000 genomes]
rs1810836	0.84[EUR][1000 genomes]
rs1888115	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2274739	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2274740	0.81[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28379831	0.85[EUR][1000 genomes]
rs28380060	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28518786	0.81[ASN][1000 genomes]
rs28580554	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28700217	0.85[EUR][1000 genomes]
rs28754733	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35760493	0.97[ASN][1000 genomes]
rs3790411	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs3790412	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3795396	0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs3806233	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3818632	0.85[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3828031	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3862047	0.80[CHD][hapmap]
rs4072425	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4351684	0.82[EUR][1000 genomes]
rs4845557	0.85[EUR][1000 genomes]
rs6427640	0.81[EUR][1000 genomes]
rs7345	0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7934	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs913860	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs913861	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs9330298	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9330299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330300	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660679	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9699949	0.94[ASN][1000 genomes]
rs9700179	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9700928	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9726753	0.96[ASN][1000 genomes]
rs9729773	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792913	0.96[ASN][1000 genomes]
rs9792963	0.96[ASN][1000 genomes]
rs9792967	0.96[ASN][1000 genomes]
rs9793310	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs985242	0.95[EUR][1000 genomes]
rs999418	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs28416529	S100A16	cis	parietal	SCAN
rs28416529	S100A10	cis	cerebellum	SCAN
rs28416529	S100A14	cis	Thyroid	GTEx
rs28416529	SLC27A3	cis	cerebellum	SCAN
rs28416529	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs28416529	S100A16	cis	cerebellum	SCAN
rs28416529	CTSS	cis	parietal	SCAN
rs28416529	RP1-178F15.4	cis	Artery Tibial	GTEx
rs28416529	CHTOP	cis	Muscle Skeletal	GTEx
rs28416529	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs28416529	S100A13	cis	lymphoblastoid	seeQTL
rs28416529	S100A13	cis	parietal	SCAN
rs28416529	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs28416529	RP1-178F15.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153585600-153596400	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:153585600-153597600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:153585600-153598800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:153585600-153599000	Weak transcription	Aorta	Aorta
5	chr1:153585800-153599200	Weak transcription	Fetal Brain Male	brain
6	chr1:153586000-153595600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:153586000-153596200	Weak transcription	Fetal Kidney	kidney
8	chr1:153586000-153598800	Weak transcription	Psoas Muscle	Psoas
9	chr1:153588600-153598800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:153589000-153596200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:153589200-153599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:153589400-153595400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:153589400-153596400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:153589400-153598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:153589600-153597800	Weak transcription	HepG2	liver
16	chr1:153590000-153598600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:153590200-153596200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:153590400-153596200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:153590400-153596200	Strong transcription	Osteobl	bone
20	chr1:153590400-153596400	Weak transcription	Liver	Liver
21	chr1:153590400-153596400	Weak transcription	Right Ventricle	heart
22	chr1:153590400-153596400	Weak transcription	Spleen	Spleen
23	chr1:153590400-153597800	Weak transcription	Right Atrium	heart
24	chr1:153590400-153598200	Weak transcription	Colonic Mucosa	Colon
25	chr1:153590400-153598200	Weak transcription	Pancreas	Pancrea
26	chr1:153590400-153598600	Weak transcription	Brain Anterior Caudate	brain
27	chr1:153590400-153598600	Weak transcription	Esophagus	oesophagus
28	chr1:153590400-153598600	Weak transcription	Gastric	stomach
29	chr1:153590400-153598600	Weak transcription	K562	blood
30	chr1:153590600-153595400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:153590600-153596200	Weak transcription	Brain Substantia Nigra	brain
32	chr1:153590600-153596200	Strong transcription	Fetal Stomach	stomach
33	chr1:153590600-153596400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:153590600-153596400	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr1:153590600-153596600	Weak transcription	Fetal Heart	heart
36	chr1:153590600-153598000	Weak transcription	Small Intestine	intestine
37	chr1:153590600-153598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:153590600-153599400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:153590800-153595400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:153590800-153596200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:153590800-153598800	Weak transcription	Stomach Mucosa	stomach
42	chr1:153591000-153595400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:153591000-153595600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:153591000-153595800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:153591000-153596200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:153591000-153596400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:153591000-153596400	Strong transcription	Placenta	Placenta
48	chr1:153591000-153598800	Strong transcription	Fetal Intestine Small	intestine
49	chr1:153591200-153596800	Strong transcription	HMEC	breast
50	chr1:153591200-153598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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