Variant report

Variant	rs2282175
Chromosome Location	chr3:119182259-119182260
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	RELA	chr3:119182234-119183100	GM12891	blood:	n/a	n/a
2	SP1	chr3:119182212-119182968	A549	lung:	n/a	chr3:119182609-119182623 chr3:119182609-119182618 chr3:119182608-119182620 chr3:119182608-119182620
3	YY1	chr3:119182046-119182959	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:119181742-119183285	GM12878	blood:	n/a	chr3:119182048-119182057
5	TCF7L2	chr3:119182000-119183133	Hela-S3	cervix:	n/a	n/a
6	SP1	chr3:119182157-119182934	A549	lung:	n/a	chr3:119182609-119182623 chr3:119182609-119182618 chr3:119182608-119182620 chr3:119182608-119182620
7	POLR2A	chr3:119182207-119183013	HUVEC	blood vessel:	n/a	n/a
8	JUND	chr3:119182259-119183073	K562	blood:	n/a	chr3:119182486-119182495
9	RELA	chr3:119182041-119183150	GM18951	blood:	n/a	n/a
10	TBP	chr3:119182243-119183309	HepG2	liver:	n/a	n/a
11	CHD1	chr3:119180705-119183081	IMR90	lung:	n/a	n/a
12	RCOR1	chr3:119182224-119183094	HepG2	liver:	n/a	n/a
13	REST	chr3:119182182-119182882	A549	lung:	n/a	n/a
14	ETS1	chr3:119182089-119182940	A549	lung:	n/a	chr3:119182638-119182651 chr3:119182636-119182650
15	MAX	chr3:119182006-119183132	A549	lung:	n/a	n/a
16	ATF3	chr3:119182115-119182840	A549	lung:	n/a	chr3:119182484-119182497 chr3:119182487-119182494 chr3:119182485-119182496 chr3:119182483-119182494 chr3:119182486-119182494 chr3:119182483-119182498 chr3:119182484-119182497 chr3:119182485-119182496 chr3:119182484-119182494 chr3:119182495-119182515 chr3:119182484-119182495 chr3:119182487-119182497 chr3:119182483-119182496 chr3:119182475-119182495 chr3:119182484-119182494
17	ATF3	chr3:119182196-119182940	A549	lung:	n/a	chr3:119182484-119182497 chr3:119182487-119182494 chr3:119182485-119182496 chr3:119182483-119182494 chr3:119182486-119182494 chr3:119182483-119182498 chr3:119182484-119182497 chr3:119182485-119182496 chr3:119182484-119182494 chr3:119182495-119182515 chr3:119182484-119182495 chr3:119182487-119182497 chr3:119182483-119182496 chr3:119182475-119182495 chr3:119182484-119182494
18	ELF1	chr3:119182000-119182758	GM12878	blood:	n/a	chr3:119182642-119182653
19	MYC	chr3:119182154-119182938	K562	blood:	n/a	n/a
20	POLR2A	chr3:119182057-119183186	GM18526	blood:	n/a	n/a
21	SIN3AK20	chr3:119182200-119182871	PANC-1	pancreas:	n/a	n/a
22	MTA3	chr3:119181718-119183385	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:119181887-119183156	GM12891	blood:	n/a	n/a
24	CEBPD	chr3:119182244-119182798	HepG2	liver:	n/a	n/a
25	TAF1	chr3:119182078-119182801	HepG2	liver:	n/a	n/a
26	SIN3AK20	chr3:119182241-119182863	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr3:119182214-119182962	K562	blood:	n/a	n/a
28	TAF1	chr3:119182210-119182896	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:119181700-119183124	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:119181971-119183198	PFSK-1	brain:	n/a	n/a
31	MXI1	chr3:119181579-119183308	SK-N-SH	brain:	n/a	n/a
32	REST	chr3:119182024-119183109	HL-60	blood:	n/a	chr3:119182990-119182999
33	POLR2A	chr3:119181727-119183311	GM12878	blood:	n/a	n/a
34	GABPA	chr3:119182227-119183023	SK-N-SH	brain:	n/a	chr3:119182567-119182581
35	GABPA	chr3:119182147-119183048	SK-N-SH	brain:	n/a	chr3:119182567-119182581
36	SP1	chr3:119182250-119182729	H1-hESC	embryonic stem cell:	n/a	chr3:119182609-119182623 chr3:119182609-119182618 chr3:119182608-119182620 chr3:119182608-119182620
37	MYC	chr3:119182217-119182825	MCF-7	breast:	n/a	n/a
38	POLR2A	chr3:119181771-119183410	MCF10A-Er-Src	breast:	n/a	n/a
39	GATA3	chr3:119182082-119183102	A549	lung:	n/a	chr3:119182660-119182667
40	PML	chr3:119181879-119183281	GM12878	blood:	n/a	n/a
41	CCNT2	chr3:119182109-119182960	K562	blood:	n/a	n/a
42	CHD2	chr3:119181963-119183210	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:119181926-119182909	Hela-S3	cervix:	n/a	n/a
44	TBP	chr3:119181951-119183182	K562	blood:	n/a	n/a
45	TCF12	chr3:119182059-119182961	ECC-1	luminal epithelium:	n/a	n/a
46	CEBPD	chr3:119182231-119182869	HepG2	liver:	n/a	n/a
47	ATF3	chr3:119182181-119182919	GM12878	blood:	n/a	chr3:119182484-119182497 chr3:119182487-119182494 chr3:119182485-119182496 chr3:119182483-119182494 chr3:119182486-119182494 chr3:119182483-119182498 chr3:119182484-119182497 chr3:119182485-119182496 chr3:119182484-119182494 chr3:119182495-119182515 chr3:119182484-119182495 chr3:119182487-119182497 chr3:119182483-119182496 chr3:119182475-119182495 chr3:119182484-119182494
48	MAX	chr3:119181948-119182988	HepG2	liver:	n/a	n/a
49	MXI1	chr3:119181563-119183030	IMR90	lung:	n/a	n/a
50	MAX	chr3:119182253-119182937	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119182037..119182735-chr7:10979846..10980807,2	Hela-S3	cervix:
2	chr16:73082165..73082838-chr3:119182253..119183080,2	Hela-S3	cervix:
3	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
4	chr2:122288414..122288963-chr3:119182081..119182951,2	NB4	blood:
5	chr17:46681489..46682463-chr3:119182153..119182746,2	Hela-S3	cervix:
6	chr3:119155062..119157702-chr3:119181053..119182622,2	MCF-7	breast:
7	chr3:119181413..119183027-chr3:119814257..119816285,2	MCF-7	breast:
8	chr3:119182092..119182964-chr7:5569083..5569895,2	Hela-S3	cervix:
9	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
10	chr2:122288293..122288864-chr3:119181979..119182744,2	Hela-S3	cervix:
11	chr3:119182042..119182653-chr9:130186618..130187243,2	Hela-S3	cervix:
12	chr1:45139479..45140296-chr3:119182033..119182625,2	Hela-S3	cervix:
13	chr3:119181455..119183728-chr3:119216896..119218706,2	MCF-7	breast:
14	chr17:56756781..56757520-chr3:119182161..119182803,2	Hela-S3	cervix:
15	chr3:119180899..119185941-chr3:119186195..119190279,17	K562	blood:
16	chr3:119181523..119183291-chr3:119394912..119396579,2	MCF-7	breast:
17	chr1:6844402..6845099-chr3:119182054..119182892,2	Hela-S3	cervix:
18	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
19	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
20	chr3:119181316..119183992-chr3:119395288..119397711,2	MCF-7	breast:

Variant related genes	Relation type
TMEM39A	TF binding region
ENSG00000176142	Chromatin interaction
ENSG00000271185	Chromatin interaction
ENSG00000140836	Chromatin interaction
ENSG00000196152	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000242622	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000108511	Chromatin interaction
ENSG00000126106	Chromatin interaction
ENSG00000264229	Chromatin interaction
ENSG00000237436	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000074054	Chromatin interaction
ENSG00000241155	Chromatin interaction
ENSG00000189043	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1132202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11556604	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12631504	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12639070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16829809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17281612	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17281647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17281703	1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2282173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57509340	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58968288	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59333081	0.93[EUR][1000 genomes]
rs59551807	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60375691	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60588168	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60671082	0.89[AMR][1000 genomes]
rs61740281	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6772534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6782411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs72968474	0.94[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	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	chr3:119180600-119182400	Active TSS	Aorta	Aorta
2	chr3:119180600-119183000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:119180600-119183200	Active TSS	Right Ventricle	heart
4	chr3:119181000-119182800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr3:119181000-119182800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr3:119181000-119182800	Active TSS	Fetal Kidney	kidney
7	chr3:119181000-119182800	Active TSS	A549	lung
8	chr3:119181000-119183000	Active TSS	Fetal Muscle Trunk	muscle
9	chr3:119181000-119183000	Active TSS	Psoas Muscle	Psoas
10	chr3:119181000-119183000	Active TSS	Right Atrium	heart
11	chr3:119181000-119183200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:119181200-119182600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:119181200-119182800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:119181200-119182800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:119181200-119182800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:119181200-119182800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr3:119181200-119182800	Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:119181200-119182800	Active TSS	Fetal Intestine Large	intestine
19	chr3:119181200-119182800	Active TSS	Fetal Intestine Small	intestine
20	chr3:119181200-119182800	Active TSS	Fetal Muscle Leg	muscle
21	chr3:119181200-119182800	Active TSS	HMEC	breast
22	chr3:119181200-119182800	Active TSS	NHLF	lung
23	chr3:119181200-119183000	Active TSS	Ovary	ovary
24	chr3:119181200-119183000	Active TSS	GM12878-XiMat	blood
25	chr3:119181200-119183000	Active TSS	K562	blood
26	chr3:119181200-119183200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:119181200-119183200	Active TSS	Stomach Mucosa	stomach
28	chr3:119181200-119183400	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:119181200-119183400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr3:119181400-119182600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:119181400-119182600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:119181400-119182600	Active TSS	Thymus	Thymus
33	chr3:119181400-119182600	Active TSS	HUVEC	blood vessel
34	chr3:119181400-119182600	Active TSS	NH-A	brain
35	chr3:119181400-119182600	Active TSS	NHEK	skin
36	chr3:119181400-119182800	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:119181400-119182800	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr3:119181400-119182800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:119181400-119182800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:119181400-119182800	Active TSS	Liver	Liver
41	chr3:119181400-119182800	Active TSS	Duodenum Mucosa	Duodenum
42	chr3:119181400-119182800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:119181400-119182800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr3:119181400-119182800	Active TSS	Fetal Lung	lung
45	chr3:119181400-119182800	Active TSS	Fetal Stomach	stomach
46	chr3:119181400-119182800	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:119181400-119182800	Active TSS	Stomach Smooth Muscle	stomach
48	chr3:119181400-119182800	Active TSS	Hela-S3	cervix
49	chr3:119181400-119182800	Active TSS	HSMM	muscle
50	chr3:119181400-119182800	Active TSS	HSMMtube	muscle

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