Variant report

Variant	rs4680344
Chromosome Location	chr3:156892462-156892463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF4	chr3:156892387-156893153	GM12878	blood:	n/a	n/a
2	BHLHE40	chr3:156892296-156893134	HepG2	liver:	n/a	n/a
3	EP300	chr3:156892170-156893265	K562	blood:	n/a	chr3:156893191-156893200 chr3:156892974-156892983
4	USF2	chr3:156892087-156893437	GM12878	blood:	n/a	n/a
5	YY1	chr3:156892249-156893343	GM12892	blood:	n/a	chr3:156892601-156892615 chr3:156892974-156892983
6	HEY1	chr3:156891630-156893320	K562	blood:	n/a	chr3:156892823-156892838
7	ATF2	chr3:156892269-156893582	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:156892184-156893349	Hela-S3	cervix:	n/a	n/a
9	FOSL2	chr3:156892437-156893165	HepG2	liver:	n/a	n/a
10	EGR1	chr3:156892397-156893126	H1-hESC	embryonic stem cell:	n/a	chr3:156892824-156892833 chr3:156892733-156892747
11	EP300	chr3:156892345-156893419	A549	lung:	n/a	chr3:156893191-156893200 chr3:156892974-156892983
12	GTF3C2	chr3:156891773-156892916	K562	blood:	n/a	n/a
13	YY1	chr3:156892438-156893333	SK-N-SH_RA	brain:	n/a	chr3:156892601-156892615 chr3:156892974-156892983
14	POLR2A	chr3:156891834-156893851	Hela-S3	cervix:	n/a	n/a
15	ZBTB33	chr3:156892451-156893294	A549	lung:	n/a	n/a
16	EP300	chr3:156892424-156893178	HepG2	liver:	n/a	chr3:156892974-156892983
17	EP300	chr3:156892248-156893270	SK-N-SH	brain:	n/a	chr3:156893191-156893200 chr3:156892974-156892983
18	BCLAF1	chr3:156892241-156893388	GM12878	blood:	n/a	chr3:156892968-156892977
19	FOXM1	chr3:156892036-156893450	GM12878	blood:	n/a	n/a
20	TBP	chr3:156892082-156893204	H1-hESC	embryonic stem cell:	n/a	n/a
21	STAT1	chr3:156892015-156893281	K562	blood:	n/a	chr3:156892751-156892762 chr3:156892747-156892767 chr3:156892633-156892641 chr3:156892750-156892764
22	REST	chr3:156892281-156893386	HL-60	blood:	n/a	n/a
23	RUNX3	chr3:156892122-156893379	GM12878	blood:	n/a	n/a
24	MYC	chr3:156892366-156893287	K562	blood:	n/a	chr3:156892666-156892676
25	MEF2A	chr3:156892373-156893230	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:156892029-156893303	HEK293	kidney:	n/a	n/a
27	GATA1	chr3:156891877-156893319	PBDE	blood:	n/a	chr3:156892055-156892065
28	POLR2A	chr3:156892060-156893832	PBDE	blood:	n/a	n/a
29	TBP	chr3:156891891-156893445	K562	blood:	n/a	n/a
30	SMARCB1	chr3:156892055-156893112	Hela-S3	cervix:	n/a	n/a
31	NFATC1	chr3:156892083-156893500	GM12878	blood:	n/a	n/a
32	ETS1	chr3:156892420-156893037	K562	blood:	n/a	chr3:156892792-156892801 chr3:156892693-156892704 chr3:156892774-156892785
33	USF2	chr3:156892348-156893273	Hela-S3	cervix:	n/a	n/a
34	SIN3AK20	chr3:156892316-156893438	HCT-116	colon:	n/a	n/a
35	POLR2A	chr3:156891881-156893806	Raji	blood:	n/a	n/a
36	GATA3	chr3:156892436-156893149	T-47D	breast:	n/a	n/a
37	NFATC1	chr3:156892364-156893486	GM12878	blood:	n/a	n/a
38	TBP	chr3:156892104-156893687	GM12878	blood:	n/a	n/a
39	NFIC	chr3:156892267-156893245	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:156892058-156893781	GM19193	blood:	n/a	n/a
41	UBTF	chr3:156892026-156893309	K562	blood:	n/a	n/a
42	CREB1	chr3:156892428-156893088	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr3:156892327-156893367	GM12878	blood:	n/a	chr3:156892601-156892615 chr3:156892974-156892983
44	ELF1	chr3:156892099-156893447	SK-N-SH	brain:	n/a	n/a
45	EGR1	chr3:156892397-156892983	K562	blood:	n/a	chr3:156892824-156892833 chr3:156892733-156892747
46	E2F6	chr3:156892256-156893394	A549	lung:	n/a	chr3:156892791-156892805 chr3:156892824-156892833
47	POLR2A	chr3:156892400-156893161	A549	lung:	n/a	n/a
48	RELA	chr3:156892346-156893666	GM18505	blood:	n/a	n/a
49	MEF2A	chr3:156892428-156893296	GM12878	blood:	n/a	n/a
50	MYC	chr3:156892203-156893310	MCF10A-Er-Src	breast:	n/a	chr3:156892666-156892676

No.	Distal block	Cell Line	Cell type
1	chr3:156892333..156892985-chrX:135962501..135963144,2	Hela-S3	cervix:
2	chr3:49449505..49450092-chr3:156892357..156893271,2	Hela-S3	cervix:
3	chr3:156891687..156894320-chr3:157219306..157221888,3	MCF-7	breast:
4	chr3:156877271..156878729-chr3:156891908..156893288,13	MCF-7	breast:
5	chr3:156877577..156878787-chr3:156892042..156894243,14	HCT-116	colon:
6	chr3:156271607..156273392-chr3:156891262..156894145,2	K562	blood:
7	chr3:156876658..156879378-chr3:156891661..156893506,34	Hela-S3	cervix:
8	chr3:156877563..156878528-chr3:156892084..156893407,12	NB4	blood:
9	chr3:156533499..156536526-chr3:156891417..156894235,3	MCF-7	breast:
10	chr3:156391446..156393768-chr3:156890974..156892598,2	MCF-7	breast:
11	chr17:66243874..66244746-chr3:156892198..156892993,2	Hela-S3	cervix:
12	chr1:19577844..19578510-chr3:156892120..156892706,2	Hela-S3	cervix:
13	chr3:156542698..156545519-chr3:156890354..156893395,4	K562	blood:
14	chr3:156877079..156878844-chr3:156892396..156893424,14	MCF-7	breast:
15	chr3:156892011..156892822-chr6:126307107..126307913,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000243176	TF binding region
RNA5SP146	TF binding region
ENSG00000163660	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000066651	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000197415	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000265100	Chromatin interaction
ENSG00000127463	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000147274	Chromatin interaction
ENSG00000053372	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000196704	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10212545	0.81[EUR][1000 genomes]
rs10451871	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10451916	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1046938	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10513507	0.82[EUR][1000 genomes]
rs11926167	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12629549	0.82[EUR][1000 genomes]
rs12637518	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12696045	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13061214	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081036	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081038	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13084070	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13084522	0.85[EUR][1000 genomes]
rs1392799	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1403103	0.84[EUR][1000 genomes]
rs1500925	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1587535	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1608127	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16827350	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16827384	0.83[EUR][1000 genomes]
rs2088814	0.82[EUR][1000 genomes]
rs2133952	0.82[EUR][1000 genomes]
rs35217153	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749214	0.84[EUR][1000 genomes]
rs4368452	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4383468	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563363	0.83[EUR][1000 genomes]
rs4632503	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4680342	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680346	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441114	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441121	0.83[EUR][1000 genomes]
rs6441122	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441123	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767619	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773061	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6780831	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6781991	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6783595	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6789178	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6805114	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6808284	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6808457	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6809003	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809394	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7620178	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7625059	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7636185	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7638194	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7642179	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7647643	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289978	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9289979	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811195	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9827676	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9831830	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9838724	0.81[EUR][1000 genomes]
rs9848409	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9849168	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858423	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861469	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9867618	0.83[EUR][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	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
2	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156891600-156893200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr3:156891800-156892600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:156891800-156892600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:156891800-156892600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr3:156891800-156892600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr3:156891800-156892600	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:156891800-156892600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:156891800-156892600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:156891800-156892600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:156891800-156892600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:156891800-156892600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:156891800-156892600	Flanking Active TSS	Dnd41	blood
13	chr3:156891800-156892600	Flanking Active TSS	Hela-S3	cervix
14	chr3:156891800-156892600	Flanking Active TSS	K562	blood
15	chr3:156891800-156892600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:156891800-156892600	Flanking Active TSS	NH-A	brain
17	chr3:156891800-156892600	Flanking Active TSS	NHEK	skin
18	chr3:156891800-156892600	Flanking Active TSS	Osteobl	bone
19	chr3:156891800-156893600	Active TSS	Brain Hippocampus Middle	brain
20	chr3:156891800-156893800	Active TSS	HSMMtube	muscle
21	chr3:156891800-156894000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:156891800-156894000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:156891800-156894000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:156891800-156894000	Active TSS	Fetal Brain Female	brain
25	chr3:156891800-156894200	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:156891800-156894200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:156891800-156894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:156891800-156894400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:156891800-156894400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:156891800-156894400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:156892000-156892600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:156892000-156892600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr3:156892000-156892600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr3:156892000-156892600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:156892000-156892600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr3:156892000-156892600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:156892000-156892600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr3:156892000-156892600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:156892000-156892600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr3:156892000-156892600	Flanking Active TSS	Placenta	Placenta
41	chr3:156892000-156892600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr3:156892000-156892600	Flanking Active TSS	HMEC	breast
43	chr3:156892000-156892600	Flanking Active TSS	HUVEC	blood vessel
44	chr3:156892000-156892800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:156892000-156893600	Active TSS	Primary T cells from cord blood	blood
46	chr3:156892000-156893600	Active TSS	Brain Angular Gyrus	brain
47	chr3:156892000-156893600	Active TSS	Brain Substantia Nigra	brain
48	chr3:156892000-156893800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:156892000-156893800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr3:156892000-156894000	Active TSS	H1 Cell Line	embryonic stem cell

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