Variant report

Variant	rs2280670
Chromosome Location	chr3:119217312-119217313
allele	A/G
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	ETS1	chr3:119217070-119217735	GM12878	blood:	n/a	chr3:119217268-119217278 chr3:119217317-119217326 chr3:119217384-119217393 chr3:119217270-119217279 chr3:119217317-119217326 chr3:119217313-119217329 chr3:119217351-119217362 chr3:119217317-119217326 chr3:119217315-119217324 chr3:119217317-119217326 chr3:119217314-119217327 chr3:119217270-119217279 chr3:119217317-119217326 chr3:119217317-119217326 chr3:119217317-119217326 chr3:119217316-119217325 chr3:119217379-119217393
2	PBX3	chr3:119217044-119217683	A549	lung:	n/a	n/a
3	TAF1	chr3:119217068-119217549	GM12878	blood:	n/a	n/a
4	NR2F2	chr3:119216911-119217724	K562	blood:	n/a	n/a
5	TAF1	chr3:119217053-119217947	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr3:119217058-119217885	H1-neurons	neurons:	n/a	n/a
7	NFATC1	chr3:119216986-119217781	GM12878	blood:	n/a	n/a
8	CREB1	chr3:119217067-119217660	H1-hESC	embryonic stem cell:	n/a	n/a
9	ELF1	chr3:119217030-119217896	MCF-7	breast:	n/a	chr3:119217315-119217326 chr3:119217271-119217280 chr3:119217270-119217281 chr3:119217270-119217281 chr3:119217313-119217326 chr3:119217316-119217325
10	BATF	chr3:119217109-119217579	GM12878	blood:	n/a	n/a
11	TAF1	chr3:119217127-119217645	HepG2	liver:	n/a	n/a
12	SIX5	chr3:119217082-119217521	GM12878	blood:	n/a	n/a
13	SP1	chr3:119217040-119217577	GM12878	blood:	n/a	chr3:119217350-119217360 chr3:119217349-119217361 chr3:119217349-119217360 chr3:119217350-119217359 chr3:119217350-119217364 chr3:119217351-119217360 chr3:119217350-119217360 chr3:119217350-119217359 chr3:119217349-119217361
14	CCNT2	chr3:119217073-119217618	K562	blood:	n/a	chr3:119217351-119217360
15	STAT3	chr3:119217196-119217494	MCF10A-Er-Src	breast:	n/a	chr3:119217384-119217391 chr3:119217398-119217405
16	POLR2A	chr3:119217057-119217889	H1-neurons	neurons:	n/a	n/a
17	TAF1	chr3:119217067-119217821	MCF-7	breast:	n/a	n/a
18	MTA3	chr3:119215802-119218062	GM12878	blood:	n/a	n/a
19	MAFK	chr3:119217179-119217657	HepG2	liver:	n/a	n/a
20	ATF3	chr3:119217074-119217531	A549	lung:	n/a	chr3:119217351-119217360 chr3:119217305-119217313
21	SIN3AK20	chr3:119217117-119217436	K562	blood:	n/a	n/a
22	CHD2	chr3:119217055-119217734	GM12878	blood:	n/a	chr3:119217349-119217359
23	MAX	chr3:119216890-119218002	A549	lung:	n/a	n/a
24	MAX	chr3:119217043-119217747	SK-N-SH	brain:	n/a	n/a
25	FOXP2	chr3:119217111-119217380	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr3:119217092-119217750	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF1	chr3:119217223-119217419	SK-N-SH_RA	brain:	n/a	n/a
28	BCL3	chr3:119216909-119217659	A549	lung:	n/a	chr3:119217351-119217364 chr3:119217270-119217279
29	PAX5	chr3:119217103-119217461	GM12878	blood:	n/a	n/a
30	CEBPB	chr3:119217047-119217635	A549	lung:	n/a	n/a
31	MAX	chr3:119217034-119217893	MCF-7	breast:	n/a	n/a
32	SRF	chr3:119217064-119217934	MCF-7	breast:	n/a	n/a
33	EP300	chr3:119216967-119217699	A549	lung:	n/a	chr3:119217271-119217278 chr3:119217318-119217325
34	FOS	chr3:119217198-119217433	MCF10A-Er-Src	breast:	n/a	n/a
35	MYC	chr3:119217062-119217729	K562	blood:	n/a	n/a
36	POLR2A	chr3:119217020-119217951	Hela-S3	cervix:	n/a	n/a
37	SIX5	chr3:119217036-119217561	A549	lung:	n/a	n/a
38	CEBPB	chr3:119217146-119217506	HepG2	liver:	n/a	n/a
39	USF2	chr3:119217121-119217786	Hela-S3	cervix:	n/a	n/a
40	TBL1XR1	chr3:119217050-119217653	GM12878	blood:	n/a	n/a
41	NFIC	chr3:119217028-119217672	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr3:119217017-119217767	HCT-116	colon:	n/a	n/a
43	POLR2A	chr3:119217020-119217909	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr3:119217015-119217925	HL-60	blood:	n/a	n/a
45	POLR2A	chr3:119217086-119217649	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:119216836-119217999	MCF10A-Er-Src	breast:	n/a	n/a
47	ELF1	chr3:119216856-119217887	HCT-116	colon:	n/a	chr3:119217315-119217326 chr3:119217271-119217280 chr3:119217270-119217281 chr3:119217270-119217281 chr3:119217313-119217326 chr3:119217316-119217325
48	EP300	chr3:119217146-119217646	K562	blood:	n/a	chr3:119217271-119217278 chr3:119217318-119217325
49	TCF7L2	chr3:119217097-119217761	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr3:119216866-119217919	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
2	chr3:118954843..118957176-chr3:119215915..119217953,2	MCF-7	breast:
3	chr3:118957609..118959509-chr3:119217273..119218823,2	MCF-7	breast:
4	chr15:67813452..67814297-chr3:119216749..119217354,2	Hela-S3	cervix:
5	chr1:149858894..149859655-chr3:119216969..119217801,2	Hela-S3	cervix:
6	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
7	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
8	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
9	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
10	chr3:119215767..119217677-chr3:119394561..119396315,2	MCF-7	breast:
11	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
12	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
13	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
14	chr16:4303462..4304222-chr3:119217111..119217705,2	Hela-S3	cervix:
15	chr3:119216891..119217847-chr3:128902758..128903410,2	Hela-S3	cervix:
16	chr3:119217063..119217701-chr5:134181325..134181902,2	NB4	blood:
17	chr3:119215904..119218714-chr3:135913674..135916504,2	MCF-7	breast:
18	chr3:119181455..119183728-chr3:119216896..119218706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272662	TF binding region
TIMMDC1	TF binding region
ENSG00000259673	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000169714	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000181904	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000262468	Chromatin interaction
ENSG00000189227	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11706028	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11706042	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11707612	0.97[ASN][1000 genomes]
rs11709468	0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11714738	0.96[ASN][1000 genomes]
rs11714843	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719448	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720158	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11720423	0.96[ASN][1000 genomes]
rs1599795	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599796	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829789	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs17203104	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17203188	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1938	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1961132	0.96[ASN][1000 genomes]
rs2049500	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2276713	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293371	0.99[ASN][1000 genomes]
rs34090996	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732418	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755579	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4447803	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4461452	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4687851	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687854	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687863	0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4688002	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4688009	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688011	1.00[CEU][hapmap];0.94[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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688013	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57506457	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59024323	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60938951	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263399	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62263404	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62263406	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62263444	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62264483	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264487	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6438534	0.93[ASN][1000 genomes]
rs6788474	0.93[ASN][1000 genomes]
rs7610335	0.91[ASN][1000 genomes]
rs9289131	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9832341	0.96[ASN][1000 genomes]
rs9850413	0.93[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr3:119216000-119218800	Active TSS	NHLF	lung
2	chr3:119216200-119217400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:119216200-119218200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:119216200-119218400	Active TSS	Brain Angular Gyrus	brain
5	chr3:119216200-119218600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:119216200-119218800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:119216200-119219200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:119216200-119219600	Active TSS	H1 Cell Line	embryonic stem cell
9	chr3:119216200-119219600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:119216200-119219800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:119216200-119220000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:119216400-119217400	Active TSS	Brain Germinal Matrix	brain
13	chr3:119216400-119218000	Active TSS	Fetal Brain Male	brain
14	chr3:119216400-119218000	Active TSS	Fetal Muscle Leg	muscle
15	chr3:119216400-119218200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:119216400-119218200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:119216400-119218200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:119216400-119218200	Active TSS	Fetal Intestine Large	intestine
19	chr3:119216400-119218200	Active TSS	Right Ventricle	heart
20	chr3:119216400-119218200	Active TSS	HSMMtube	muscle
21	chr3:119216400-119218200	Active TSS	NH-A	brain
22	chr3:119216400-119218400	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr3:119216400-119218400	Active TSS	Rectal Smooth Muscle	rectum
24	chr3:119216400-119218800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:119216400-119219200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:119216400-119219400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr3:119216400-119219600	Active TSS	Psoas Muscle	Psoas
28	chr3:119216400-119220200	Active TSS	K562	blood
29	chr3:119216600-119217600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:119216600-119217800	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:119216600-119217800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:119216600-119217800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr3:119216600-119218000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:119216600-119218000	Active TSS	Aorta	Aorta
35	chr3:119216600-119218000	Active TSS	Fetal Lung	lung
36	chr3:119216600-119218000	Active TSS	Fetal Muscle Trunk	muscle
37	chr3:119216600-119218000	Active TSS	Gastric	stomach
38	chr3:119216600-119218000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:119216600-119218000	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr3:119216600-119218000	Active TSS	Stomach Mucosa	stomach
41	chr3:119216600-119218200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:119216600-119218200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:119216600-119218200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:119216600-119218200	Active TSS	Esophagus	oesophagus
45	chr3:119216600-119218200	Active TSS	Fetal Intestine Small	intestine
46	chr3:119216600-119218200	Active TSS	Lung	lung
47	chr3:119216600-119218200	Active TSS	Ovary	ovary
48	chr3:119216600-119218200	Active TSS	Pancreas	Pancrea
49	chr3:119216600-119218200	Active TSS	Right Atrium	heart
50	chr3:119216600-119218200	Active TSS	NHEK	skin

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