Variant report

Variant	rs724016
Chromosome Location	chr3:141105570-141105571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:141105512-141106032	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:141104639-141106041	ProgFib	skin:	n/a	n/a
3	CHD1	chr3:141104709-141108325	GM12878	blood:	n/a	n/a
4	JUND	chr3:141105498-141105942	K562	blood:	n/a	n/a
5	POLR2A	chr3:141105458-141105736	K562	blood:	n/a	n/a
6	POLR2A	chr3:141104500-141106316	U87	brain:	n/a	n/a
7	REST	chr3:141104388-141107025	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr3:141104880-141106178	GM12878	blood:	n/a	n/a
9	STAT5A	chr3:141104407-141106765	GM12878	blood:	n/a	chr3:141104969-141104981 chr3:141104686-141104698
10	POLR2A	chr3:141104282-141106914	GM12878	blood:	n/a	n/a
11	CEBPB	chr3:141105497-141106084	K562	blood:	n/a	n/a
12	CUX1	chr3:141105424-141105814	K562	blood:	n/a	n/a
13	POLR2A	chr3:141102275-141108652	GM12892	blood:	n/a	n/a
14	NFATC1	chr3:141104559-141106126	GM12878	blood:	n/a	n/a
15	MXI1	chr3:141103587-141107076	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:141104427-141106788	GM15510	blood:	n/a	n/a
17	NFIC	chr3:141102247-141106881	GM12878	blood:	n/a	chr3:141104154-141104170
18	TAF1	chr3:141105427-141106085	GM12878	blood:	n/a	n/a
19	MAFK	chr3:141105183-141105900	K562	blood:	n/a	n/a
20	POLR2A	chr3:141101616-141105956	IMR90	lung:	n/a	n/a
21	POLR2A	chr3:141103827-141106384	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr3:141102361-141107014	U87	brain:	n/a	n/a
23	ATF3	chr3:141105490-141105870	K562	blood:	n/a	n/a
24	TBP	chr3:141105438-141106830	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:141104605-141106814	Raji	blood:	n/a	n/a
26	MTA3	chr3:141102180-141106932	GM12878	blood:	n/a	n/a
27	FOXP2	chr3:141105507-141106079	SK-N-MC	brain:	n/a	n/a
28	CEBPB	chr3:141105565-141106131	HepG2	liver:	n/a	n/a
29	KAP1	chr3:141105134-141106225	U2OS	brain:	n/a	n/a
30	MAX	chr3:141105568-141105986	K562	blood:	n/a	n/a
31	ATF2	chr3:141105332-141106803	GM12878	blood:	n/a	n/a
32	YY1	chr3:141105449-141106063	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:141105346-141106143	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr3:141105518-141105930	K562	blood:	n/a	n/a
35	PML	chr3:141104255-141106832	GM12878	blood:	n/a	n/a
36	RCOR1	chr3:141105509-141105958	K562	blood:	n/a	n/a
37	TEAD4	chr3:141105404-141106077	K562	blood:	n/a	n/a
38	POLR2A	chr3:141101478-141106905	GM19099	blood:	n/a	n/a
39	POLR2A	chr3:141104500-141106687	U87	brain:	n/a	n/a
40	POLR2A	chr3:141101516-141106882	GM12878	blood:	n/a	n/a
41	YY1	chr3:141105541-141106071	GM12878	blood:	n/a	n/a
42	RFX5	chr3:141105531-141105919	GM12878	blood:	n/a	n/a
43	ATF1	chr3:141105534-141105951	K562	blood:	n/a	n/a
44	POLR2A	chr3:141104136-141106779	GM12892	blood:	n/a	n/a
45	MAFK	chr3:141104218-141106044	IMR90	lung:	n/a	chr3:141104417-141104437 chr3:141104393-141104413 chr3:141104867-141104882 chr3:141104392-141104407 chr3:141104395-141104411 chr3:141104417-141104428
46	POLR2A	chr3:141104553-141106659	GM18526	blood:	n/a	n/a
47	NFIC	chr3:141104539-141105984	GM12878	blood:	n/a	n/a
48	MTA3	chr3:141105332-141106842	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:141105465-141106035	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:141102232-141107020	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141086746..141089442-chr3:141102578..141106319,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-3	chr3:141105284-141105597	NONHSAT092430
2	lnc-ACPL2-3	chr3:141105288-141105779	NONHSAT092431

No data

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13068733	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13077048	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1344672	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1344674	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1346408	0.81[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1863868	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1991431	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2871960	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683605	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4683606	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57345461	0.98[ASN][1000 genomes]
rs58473751	0.98[ASN][1000 genomes]
rs6440003	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6763931	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764769	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6785012	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7625643	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7632381	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7650602	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853018	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9856584	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:4)

Disease	PMID	Source
Height	20881960	GWAS catalog
Height	18391950	GWAS catalog
Height	18193045	GWAS catalog
Infant length	25281659	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs724016	ZBTB38	cis	cerebellum	SCAN
rs724016	RASA2	cis	cerebellum	SCAN
rs724016	SPSB4	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
2	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
3	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
4	chr3:141089600-141105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:141091000-141107200	Weak transcription	Liver	Liver
6	chr3:141092000-141105600	Weak transcription	Gastric	stomach
7	chr3:141094800-141105600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:141094800-141112200	Weak transcription	Spleen	Spleen
9	chr3:141095200-141105600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:141095200-141105800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:141096000-141111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:141096200-141106400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:141097200-141105600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:141098400-141105800	Weak transcription	Right Ventricle	heart
15	chr3:141098400-141107600	Weak transcription	Aorta	Aorta
16	chr3:141098600-141105600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:141098600-141115200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:141099000-141110400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:141099400-141105800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:141099400-141106600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:141099600-141109800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:141099800-141106800	Strong transcription	Left Ventricle	heart
23	chr3:141100600-141112400	Weak transcription	Lung	lung
24	chr3:141101800-141105800	Genic enhancers	A549	lung
25	chr3:141102000-141105600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:141102400-141105600	Enhancers	Fetal Kidney	kidney
27	chr3:141102400-141107600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:141102600-141105600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr3:141102800-141105600	Weak transcription	Colonic Mucosa	Colon
30	chr3:141102800-141105800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:141102800-141111800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:141102800-141112000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:141103200-141107000	Genic enhancers	Osteobl	bone
34	chr3:141103200-141107600	Weak transcription	Hela-S3	cervix
35	chr3:141103200-141107800	Weak transcription	Stomach Mucosa	stomach
36	chr3:141103200-141111000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:141103400-141105600	Weak transcription	HSMMtube	muscle
38	chr3:141103600-141105600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:141103600-141105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:141103600-141105600	Weak transcription	Esophagus	oesophagus
41	chr3:141103600-141105800	Weak transcription	Placenta	Placenta
42	chr3:141103600-141105800	Weak transcription	HUVEC	blood vessel
43	chr3:141103600-141106800	Strong transcription	NH-A	brain
44	chr3:141103600-141107800	Strong transcription	HSMM	muscle
45	chr3:141103600-141110200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:141103800-141105600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:141103800-141105600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:141103800-141105600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:141103800-141105600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:141103800-141105800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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