Variant report

Variant	rs72940078
Chromosome Location	chr3:112279916-112279917
allele	G/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	POLR2A	chr3:112279834-112281538	NB4	blood:	n/a	n/a
2	TBP	chr3:112279682-112280170	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr3:112279851-112281583	ECC-1	luminal epithelium:	n/a	n/a
4	RUNX3	chr3:112279815-112281482	GM12878	blood:	n/a	n/a
5	NFIC	chr3:112279693-112281548	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr3:112279863-112281529	SK-N-SH	brain:	n/a	n/a
7	MAX	chr3:112279763-112281627	A549	lung:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
8	TAF1	chr3:112279812-112280210	K562	blood:	n/a	n/a
9	POLR2A	chr3:112279756-112280265	HUVEC	blood vessel:	n/a	n/a
10	MYC	chr3:112279856-112281492	MCF10A-Er-Src	breast:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
11	POLR2A	chr3:112279610-112281668	U87	brain:	n/a	n/a
12	CHD2	chr3:112279897-112281267	H1-hESC	embryonic stem cell:	n/a	n/a
13	MXI1	chr3:112279681-112281770	GM12878	blood:	n/a	n/a
14	ELK1	chr3:112279784-112280038	K562	blood:	n/a	n/a
15	USF2	chr3:112279646-112281456	Hela-S3	cervix:	n/a	chr3:112280795-112280808 chr3:112280819-112280828 chr3:112280797-112280806 chr3:112280798-112280807 chr3:112280820-112280829 chr3:112280796-112280807 chr3:112280819-112280830 chr3:112280821-112280830 chr3:112280820-112280829 chr3:112280818-112280831 chr3:112280797-112280806
16	MAX	chr3:112279832-112281520	MCF-7	breast:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
17	MXI1	chr3:112279150-112282285	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:112279777-112281540	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr3:112279886-112280200	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:112279738-112281601	SK-N-MC	brain:	n/a	n/a
21	ELF1	chr3:112279778-112281370	SK-N-SH	brain:	n/a	n/a
22	RELA	chr3:112279915-112281544	GM18951	blood:	n/a	n/a
23	MTA3	chr3:112279722-112280501	GM12878	blood:	n/a	n/a
24	MAX	chr3:112279861-112281554	A549	lung:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
25	POLR2A	chr3:112279833-112281524	H1-neurons	neurons:	n/a	n/a
26	JUND	chr3:112279792-112280246	K562	blood:	n/a	n/a
27	MTA3	chr3:112279769-112281614	GM12878	blood:	n/a	n/a
28	TAF1	chr3:112279915-112281447	K562	blood:	n/a	n/a
29	ZNF143	chr3:112279853-112281508	K562	blood:	n/a	n/a
30	BCLAF1	chr3:112279687-112281617	GM12878	blood:	n/a	chr3:112280274-112280282 chr3:112280841-112280854
31	PML	chr3:112279648-112281767	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:112279810-112280229	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:112279771-112281577	HL-60	blood:	n/a	n/a
34	POLR2A	chr3:112279835-112280304	GM12891	blood:	n/a	n/a
35	POLR2A	chr3:112279777-112281518	K562	blood:	n/a	n/a
36	SIN3AK20	chr3:112279833-112280166	A549	lung:	n/a	n/a
37	TAF1	chr3:112279743-112280473	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAZ	chr3:112279706-112281716	IMR90	lung:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
39	POLR2A	chr3:112279865-112281478	K562	blood:	n/a	n/a
40	POLR2A	chr3:112279862-112281777	GM18951	blood:	n/a	n/a
41	TAF1	chr3:112279856-112280210	H1-hESC	embryonic stem cell:	n/a	n/a
42	SIN3AK20	chr3:112279897-112280455	H1-hESC	embryonic stem cell:	n/a	n/a
43	MXI1	chr3:112279859-112281485	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:112279903-112280152	SK-N-SH	brain:	n/a	n/a
45	CREB1	chr3:112279780-112280330	ECC-1	luminal epithelium:	n/a	n/a
46	MAX	chr3:112279841-112281554	ECC-1	luminal epithelium:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
47	HCFC1	chr3:112279705-112281402	K562	blood:	n/a	n/a
48	POLR2A	chr3:112279700-112281551	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:112279834-112281515	K562	blood:	n/a	n/a
50	POLR2A	chr3:112279741-112281532	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:73150272..73150774-chr3:112279377..112280194,2	Hela-S3	cervix:
2	chr3:112278908..112280422-chr3:112332975..112334877,2	MCF-7	breast:
3	chr17:47841055..47841749-chr3:112279742..112280576,2	NB4	blood:
4	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
5	chr3:111697752..111700080-chr3:112279042..112280721,2	K562	blood:
6	chr3:112279683..112282381-chr3:112710182..112712390,2	K562	blood:
7	chr1:144533692..144534204-chr3:112279831..112280562,2	Hela-S3	cervix:
8	chr3:111803332..111805315-chr3:112279253..112281220,2	MCF-7	breast:
9	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
10	chr3:112277732..112280310-chr3:112708635..112710146,2	K562	blood:
11	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
12	chr3:112253490..112256363-chr3:112279039..112281187,3	K562	blood:
13	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
14	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
15	chr3:111830456..111832040-chr3:112279153..112281688,2	K562	blood:
16	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
17	chr3:112257078..112259281-chr3:112279236..112282506,3	MCF-7	breast:
18	chr3:112272255..112274870-chr3:112277581..112280165,3	K562	blood:

Variant related genes	Relation type
SLC35A5	TF binding region
ENSG00000091986	Chromatin interaction
ENSG00000207940	Chromatin interaction
ENSG00000121104	Chromatin interaction
ENSG00000163611	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000144827	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000114529	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13070342	0.94[AFR][1000 genomes]
rs57937078	1.00[AMR][1000 genomes]
rs59090018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938420	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938422	1.00[AMR][1000 genomes]
rs72938432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938438	1.00[AMR][1000 genomes]
rs72938454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942068	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942074	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942089	1.00[AMR][1000 genomes]
rs72943904	1.00[AMR][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	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	24 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	chr3:112278200-112280000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:112278200-112280800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:112278200-112282000	Active TSS	K562	blood
4	chr3:112278200-112282200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:112278400-112280000	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr3:112278400-112280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr3:112278400-112280000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:112278400-112282200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:112278600-112280000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr3:112278600-112282400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:112278600-112283800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:112278800-112280000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr3:112278800-112280800	Active TSS	Right Atrium	heart
14	chr3:112278800-112281600	Active TSS	Fetal Thymus	thymus
15	chr3:112278800-112281800	Active TSS	Thymus	Thymus
16	chr3:112278800-112282000	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr3:112278800-112282000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr3:112278800-112282000	Active TSS	HSMM	muscle
19	chr3:112278800-112282200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr3:112278800-112282200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:112278800-112282200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:112278800-112282200	Active TSS	Psoas Muscle	Psoas
23	chr3:112279000-112280200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:112279000-112282000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:112279000-112282000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:112279000-112282000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:112279000-112282000	Active TSS	Fetal Intestine Large	intestine
28	chr3:112279000-112282000	Active TSS	Fetal Intestine Small	intestine
29	chr3:112279000-112282000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr3:112279000-112282000	Active TSS	GM12878-XiMat	blood
31	chr3:112279000-112282000	Active TSS	HMEC	breast
32	chr3:112279000-112282200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:112279000-112282200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr3:112279000-112282200	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:112279000-112282200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:112279000-112282400	Active TSS	NHLF	lung
37	chr3:112279000-112282600	Active TSS	NHDF-Ad	bronchial
38	chr3:112279200-112280000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr3:112279200-112280000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr3:112279200-112281200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:112279200-112281600	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr3:112279200-112281600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:112279200-112281800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:112279200-112281800	Active TSS	Fetal Muscle Leg	muscle
45	chr3:112279200-112281800	Active TSS	Fetal Stomach	stomach
46	chr3:112279200-112282000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:112279200-112282000	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:112279200-112282000	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr3:112279200-112282200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:112279200-112282200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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