Variant report

Variant	rs4680342
Chromosome Location	chr3:156873220-156873221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156871943-156873244	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:156872516-156873496	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:156861007-156879269	K562	blood:	n/a	n/a
4	POLR2A	chr3:156863231-156878853	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:156868728-156873222	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:156872238-156873494	Hela-S3	cervix:	n/a	n/a
7	CHD1	chr3:156868741-156879284	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:156863168-156879174	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:156873171-156873563	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156872801..156875141-chr3:156917968..156922076,3	K562	blood:
2	chr3:156543622..156545874-chr3:156870977..156873628,2	MCF-7	breast:
3	chr3:156267016..156271448-chr3:156870182..156873447,4	K562	blood:
4	chr3:156267109..156271448-chr3:156870440..156873447,4	K562	blood:

No data

Variant related genes	Relation type
CCNL1	TF binding region
ENSG00000114850	Chromatin interaction
ENSG00000197980	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10212545	0.85[EUR][1000 genomes]
rs10451871	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10451916	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1046938	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10513507	0.92[CEU][hapmap]
rs1060543	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap]
rs1157738	0.81[CEU][hapmap]
rs11926167	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629549	0.88[EUR][1000 genomes]
rs12637518	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12696045	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13061214	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs13081036	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs13081038	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13084070	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13084522	0.81[EUR][1000 genomes]
rs1392799	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1403104	0.81[CEU][hapmap]
rs1500925	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1587534	0.84[EUR][1000 genomes]
rs1587535	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.82[ASN][1000 genomes]
rs1608127	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.82[ASN][1000 genomes]
rs16827308	0.81[CEU][hapmap];0.87[YRI][hapmap]
rs16827322	0.81[CEU][hapmap]
rs16827350	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2088814	0.88[EUR][1000 genomes]
rs2133952	0.88[EUR][1000 genomes]
rs28384296	0.82[EUR][1000 genomes]
rs35217153	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749214	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap]
rs4368452	0.89[EUR][1000 genomes]
rs4383468	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4563363	0.89[EUR][1000 genomes]
rs4632503	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680344	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680346	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680347	0.83[CEU][hapmap]
rs4680348	0.84[EUR][1000 genomes]
rs6441114	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441121	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6441122	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441123	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.82[ASN][1000 genomes]
rs67196056	0.85[EUR][1000 genomes]
rs6767619	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773061	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6780831	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6781991	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6783595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6789178	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6805114	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808284	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6808457	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6809003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6809394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620178	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7625059	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs7636185	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7638194	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7642179	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7647643	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924517	0.85[CEU][hapmap]
rs9289978	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9289979	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9811195	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9827676	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831830	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9838724	0.87[EUR][1000 genomes]
rs9848409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849168	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9858423	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861469	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9867618	0.85[CEU][hapmap];0.89[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	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:156852600-156873400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr3:156855400-156877000	Weak transcription	Gastric	stomach
4	chr3:156856000-156874600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:156858400-156876400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:156859400-156876200	Strong transcription	Placenta	Placenta
7	chr3:156860000-156874000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:156861600-156873800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:156861800-156875600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr3:156863200-156876800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:156864000-156875600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:156864800-156874600	Strong transcription	Fetal Thymus	thymus
13	chr3:156865400-156873600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:156865800-156874200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:156866200-156877000	Weak transcription	Esophagus	oesophagus
16	chr3:156866400-156874600	Weak transcription	Pancreas	Pancrea
17	chr3:156866400-156877000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:156867200-156875600	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:156867800-156874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:156869000-156874400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:156869000-156874600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:156869800-156874600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:156869800-156874600	Weak transcription	Spleen	Spleen
24	chr3:156869800-156876600	Weak transcription	Lung	lung
25	chr3:156870000-156874600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:156870400-156874600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:156870800-156874000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:156870800-156874400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:156870800-156875600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:156870800-156877000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
31	chr3:156871000-156877000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156871000-156877000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
33	chr3:156871400-156874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:156871400-156874600	Weak transcription	Left Ventricle	heart
35	chr3:156871400-156875600	Genic enhancers	Fetal Lung	lung
36	chr3:156871400-156877000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:156871600-156873400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:156871600-156874400	Enhancers	Fetal Intestine Small	intestine
39	chr3:156871600-156875200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:156871600-156875400	Enhancers	Fetal Heart	heart
41	chr3:156871600-156876400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:156871600-156876800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
43	chr3:156871600-156877200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:156871600-156877200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
45	chr3:156871800-156873600	Enhancers	Brain Anterior Caudate	brain
46	chr3:156871800-156874000	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:156871800-156874400	Active TSS	Psoas Muscle	Psoas
48	chr3:156871800-156874600	Weak transcription	Colonic Mucosa	Colon
49	chr3:156871800-156876800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:156871800-156877000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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