Variant report

Variant	rs4928169
Chromosome Location	chr3:100034849-100034850
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100033941..100036861-chr3:100119084..100121565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1036770	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11915985	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1214369	0.88[EUR][1000 genomes]
rs1214371	0.85[ASN][1000 genomes]
rs1214372	0.89[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs1214373	0.89[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs12696084	0.84[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs13070392	0.89[CEU][hapmap]
rs1609481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028494	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2029162	1.00[CHB][hapmap]
rs277636	0.88[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs277637	1.00[CHB][hapmap]
rs277652	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs277654	0.88[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs277655	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs3772698	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs384528	0.85[ASN][1000 genomes]
rs4345098	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4552390	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928118	1.00[CHB][hapmap]
rs4928119	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62281675	0.84[EUR][1000 genomes]
rs6763594	0.84[EUR][1000 genomes]
rs6802765	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6804963	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs6808175	0.83[EUR][1000 genomes]
rs7427443	0.83[EUR][1000 genomes]
rs7618677	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7630257	0.84[EUR][1000 genomes]
rs7637157	0.89[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7638503	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931332	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs967608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9863237	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9863738	0.89[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9880795	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9882337	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4928169	ZPLD1	cis	parietal	SCAN
rs4928169	TBC1D23	cis	Muscle Skeletal	GTEx
rs4928169	ZNF546	trans	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
4	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
6	chr3:100007000-100045000	Weak transcription	Lung	lung
7	chr3:100007800-100035800	Weak transcription	A549	lung
8	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
9	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:100014600-100042200	Weak transcription	Fetal Brain Male	brain
11	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:100018800-100035800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:100019000-100043200	Weak transcription	Brain Angular Gyrus	brain
14	chr3:100019200-100038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
16	chr3:100020000-100038600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
19	chr3:100021200-100035600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:100021200-100036000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
23	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
25	chr3:100025800-100038800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
28	chr3:100026000-100035600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:100026000-100038600	Weak transcription	HMEC	breast
30	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
32	chr3:100026200-100038600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:100026400-100035600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:100026400-100035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:100026400-100038400	Weak transcription	Ovary	ovary
36	chr3:100026400-100038600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:100026400-100038600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:100026400-100038800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:100026400-100038800	Weak transcription	K562	blood
40	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
41	chr3:100026400-100052800	Weak transcription	NHEK	skin
42	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:100029200-100038200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:100029200-100038400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:100029400-100035200	Strong transcription	NH-A	brain
48	chr3:100029400-100037600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:100029400-100038400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:100029400-100038600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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