Variant report

Variant	rs4680340
Chromosome Location	chr3:156861460-156861461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156851307..156853070-chr3:156861254..156863346,2	MCF-7	breast:
2	chr3:156860100..156862214-chr3:156863800..156865338,3	MCF-7	breast:
3	chr3:156266499..156269259-chr3:156860290..156863068,2	K562	blood:
4	chr3:156829814..156832338-chr3:156860168..156861958,2	K562	blood:

Variant related genes	Relation type
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10513508	0.91[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs10755111	0.82[CHB][hapmap]
rs10936061	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936062	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936064	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936065	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936067	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936068	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936069	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936074	0.87[EUR][1000 genomes]
rs10936078	0.89[CEU][hapmap]
rs10936080	0.91[CEU][hapmap]
rs10936081	0.91[CEU][hapmap]
rs1157738	0.86[CEU][hapmap]
rs12488480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489453	0.88[EUR][1000 genomes]
rs12489799	0.90[EUR][1000 genomes]
rs12490836	0.91[EUR][1000 genomes]
rs12492801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496051	0.88[EUR][1000 genomes]
rs12496111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12497891	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630209	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632562	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs12633429	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap]
rs12634818	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12635088	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12636125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403104	0.87[CEU][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap]
rs1403105	0.82[CHB][hapmap]
rs1403106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs1403108	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs1500924	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs1522392	0.91[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs1568611	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs16827308	0.87[CEU][hapmap]
rs16827318	0.88[EUR][1000 genomes]
rs16827322	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs16827352	0.87[EUR][1000 genomes]
rs17552941	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1995304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2047648	0.86[CEU][hapmap]
rs2321740	0.82[EUR][1000 genomes]
rs2321743	0.82[CHB][hapmap]
rs2874616	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs35910014	0.88[EUR][1000 genomes]
rs3935750	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41272613	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4371471	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4383467	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4413278	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4608646	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4679790	0.82[CHB][hapmap]
rs4679791	0.82[CHB][hapmap]
rs4680343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680347	0.86[CEU][hapmap]
rs4680352	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs4680353	0.82[CHB][hapmap]
rs4680354	0.90[CEU][hapmap]
rs5003893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55828309	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55835412	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55949516	0.91[EUR][1000 genomes]
rs55953639	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56078410	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56263456	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57322659	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57511361	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59210914	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59279023	0.87[EUR][1000 genomes]
rs59485606	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59865540	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60153077	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61149035	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62274129	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62274155	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62274156	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62274159	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276460	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276461	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276462	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62276465	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276470	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62276471	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276474	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276475	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276479	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62276480	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276488	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62276489	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62276490	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276491	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276495	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276496	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276497	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276501	0.90[EUR][1000 genomes]
rs62276502	0.90[EUR][1000 genomes]
rs62276504	0.88[EUR][1000 genomes]
rs62276505	0.87[EUR][1000 genomes]
rs6441115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441119	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6767619	0.82[CEU][hapmap]
rs6768052	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6780205	0.87[EUR][1000 genomes]
rs6781682	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788214	1.00[CEU][hapmap]
rs6792479	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6799567	0.91[CEU][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs6805989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806232	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154633	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73154649	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73154657	0.91[EUR][1000 genomes]
rs73154659	0.88[EUR][1000 genomes]
rs73154671	0.81[EUR][1000 genomes]
rs73873800	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7621912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7626589	0.90[EUR][1000 genomes]
rs7631257	0.91[CEU][hapmap]
rs7633004	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7648599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs7649737	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs7652298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs8180056	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8180057	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4680340	SMC4	cis	parietal	SCAN
rs4680340	PTX3	cis	parietal	SCAN
rs4680340	PTX3	cis	cerebellum	SCAN
rs4680340	IL12A	cis	cerebellum	SCAN
rs4680340	CCNL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:156849000-156861800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:156849000-156862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:156849200-156861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:156849200-156861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:156849400-156861600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:156850400-156861600	Weak transcription	Hela-S3	cervix
11	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:156853200-156865400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:156853400-156872000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:156855000-156865800	Weak transcription	Aorta	Aorta
15	chr3:156855000-156866000	Weak transcription	Ovary	ovary
16	chr3:156855000-156872000	Weak transcription	Right Atrium	heart
17	chr3:156855200-156861600	Weak transcription	Psoas Muscle	Psoas
18	chr3:156855200-156861800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:156855200-156862000	Weak transcription	Pancreas	Pancrea
20	chr3:156855200-156862200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:156855400-156862000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:156855400-156862200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:156855400-156862200	Weak transcription	HSMMtube	muscle
24	chr3:156855400-156865400	Weak transcription	Fetal Brain Male	brain
25	chr3:156855400-156865800	Weak transcription	Colonic Mucosa	Colon
26	chr3:156855400-156866000	Weak transcription	Fetal Heart	heart
27	chr3:156855400-156877000	Weak transcription	Gastric	stomach
28	chr3:156855600-156861600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:156855600-156861600	Weak transcription	Fetal Kidney	kidney
30	chr3:156855600-156862000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:156855600-156862000	Weak transcription	HMEC	breast
32	chr3:156855600-156862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:156855600-156862200	Weak transcription	K562	blood
34	chr3:156855600-156863200	Weak transcription	NH-A	brain
35	chr3:156855600-156863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:156855600-156863600	Weak transcription	Brain Angular Gyrus	brain
37	chr3:156855600-156864200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:156855600-156865400	Weak transcription	HepG2	liver
39	chr3:156855600-156865800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:156855600-156865800	Weak transcription	NHLF	lung
41	chr3:156855600-156866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:156855600-156867200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:156855800-156861600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:156855800-156862000	Weak transcription	NHEK	skin
45	chr3:156855800-156865800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:156855800-156867400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:156856000-156863800	Weak transcription	Stomach Mucosa	stomach
48	chr3:156856000-156870800	Strong transcription	Primary T cells from cord blood	blood
49	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:156857200-156864000	Strong transcription	Left Ventricle	heart

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