Variant report

Variant	rs72940083
Chromosome Location	chr3:112281038-112281039
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	POLR2A	chr3:112279834-112281538	NB4	blood:	n/a	n/a
2	CREB1	chr3:112280587-112281082	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:112280054-112281464	GM10847	blood:	n/a	n/a
4	ATF3	chr3:112280500-112281132	H1-hESC	embryonic stem cell:	n/a	chr3:112280797-112280806 chr3:112280786-112280806
5	MAX	chr3:112280609-112281320	K562	blood:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
6	POLR2A	chr3:112280004-112281476	A549	lung:	n/a	n/a
7	SIN3AK20	chr3:112280501-112281157	HepG2	liver:	n/a	n/a
8	ATF3	chr3:112280563-112281302	A549	lung:	n/a	chr3:112280797-112280806 chr3:112280786-112280806
9	TAF1	chr3:112279851-112281583	ECC-1	luminal epithelium:	n/a	n/a
10	JUND	chr3:112280568-112281488	K562	blood:	n/a	n/a
11	RUNX3	chr3:112279815-112281482	GM12878	blood:	n/a	n/a
12	TAF1	chr3:112280527-112281325	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFIC	chr3:112279693-112281548	GM12878	blood:	n/a	n/a
14	CEBPB	chr3:112280783-112281074	K562	blood:	n/a	n/a
15	MXI1	chr3:112279921-112281615	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr3:112279863-112281529	SK-N-SH	brain:	n/a	n/a
17	USF1	chr3:112280397-112281433	A549	lung:	n/a	chr3:112280795-112280808 chr3:112280819-112280828 chr3:112280797-112280806 chr3:112280798-112280807 chr3:112280820-112280829 chr3:112280821-112280830 chr3:112280820-112280829 chr3:112280818-112280831 chr3:112280797-112280806
18	USF1	chr3:112280521-112281069	SK-N-SH_RA	brain:	n/a	chr3:112280795-112280808 chr3:112280819-112280828 chr3:112280797-112280806 chr3:112280798-112280807 chr3:112280820-112280829 chr3:112280821-112280830 chr3:112280820-112280829 chr3:112280818-112280831 chr3:112280797-112280806
19	MYC	chr3:112280709-112281468	MCF10A-Er-Src	breast:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
20	CEBPB	chr3:112280702-112281554	K562	blood:	n/a	n/a
21	POLR2A	chr3:112279964-112281462	MCF-7	breast:	n/a	n/a
22	MAX	chr3:112279763-112281627	A549	lung:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
23	FOS	chr3:112280603-112281232	GM12878	blood:	n/a	n/a
24	SMC3	chr3:112279926-112281487	Hela-S3	cervix:	n/a	n/a
25	EP300	chr3:112280653-112281422	SK-N-SH_RA	brain:	n/a	n/a
26	MYC	chr3:112279856-112281492	MCF10A-Er-Src	breast:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
27	POLR2A	chr3:112279610-112281668	U87	brain:	n/a	n/a
28	CEBPB	chr3:112280412-112281674	GM12878	blood:	n/a	n/a
29	ELF1	chr3:112279955-112281412	GM12878	blood:	n/a	n/a
30	GABPA	chr3:112280530-112281405	A549	lung:	n/a	chr3:112281144-112281158 chr3:112281191-112281200 chr3:112281191-112281202 chr3:112281188-112281202
31	EP300	chr3:112280568-112281508	GM12878	blood:	n/a	n/a
32	CHD2	chr3:112279897-112281267	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr3:112279681-112281770	GM12878	blood:	n/a	n/a
34	ELF1	chr3:112280240-112281542	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:112280327-112281538	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:112280353-112281393	A549	lung:	n/a	n/a
37	HEY1	chr3:112280560-112281487	HepG2	liver:	n/a	chr3:112280841-112280856
38	RCOR1	chr3:112280664-112281431	K562	blood:	n/a	n/a
39	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
40	MAX	chr3:112279832-112281520	MCF-7	breast:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
41	SP1	chr3:112280573-112281074	H1-hESC	embryonic stem cell:	n/a	chr3:112280975-112280989 chr3:112280847-112280858 chr3:112280835-112280842 chr3:112280978-112280990 chr3:112280868-112280879 chr3:112280978-112280990
42	MAX	chr3:112280055-112281456	HepG2	liver:	n/a	chr3:112280797-112280806 chr3:112280979-112280989 chr3:112280820-112280829
43	MXI1	chr3:112279150-112282285	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr3:112279777-112281540	Hela-S3	cervix:	n/a	n/a
45	MYC	chr3:112280966-112281040	GM12878	blood:	n/a	chr3:112280979-112280989
46	PML	chr3:112280546-112281401	K562	blood:	n/a	n/a
47	POLR2A	chr3:112280364-112281483	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:112279738-112281601	SK-N-MC	brain:	n/a	n/a
49	ELF1	chr3:112279778-112281370	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr3:112280315-112281554	SK-N-MC	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:112281021-112281071	AG04450	lung:	fetal
2	chr3:112281021-112281071	AG09309	skin:	n/a
3	chr3:112281021-112281071	HL-60	blood:	n/a
4	chr3:112281021-112281071	GM12891	blood:	n/a
5	chr3:112281021-112281071	GM12892	blood:	n/a
6	chr3:112281021-112281071	Jurkat	blood:	n/a
7	chr3:112281021-112281071	HRCEpiC	kidney:	n/a
8	chr3:112281021-112281071	HRPEpiC	eye:	n/a
9	chr3:112281021-112281071	AG10803	skin:	n/a
10	chr3:112281021-112281071	Hela-S3	cervix:	n/a
11	chr3:112281021-112281071	LNCaP	prostate:	n/a
12	chr3:112281021-112281071	RPTEC	kidney:	n/a
13	chr3:112281021-112281071	SK-N-MC	brain:	n/a
14	chr3:112281021-112281071	HepG2	liver:	n/a
15	chr3:112281021-112281071	HNPCEpiC	eye:	n/a
16	chr3:112281021-112281071	HEK293	kidney:	embryo
17	chr3:112281021-112281071	BE2_C	brain:	n/a
18	chr3:112281021-112281071	ECC-1	luminal epithelium:	n/a
19	chr3:112281021-112281071	HCT-116	colon:	n/a
20	chr3:112281021-112281071	PANC-1	pancreas:	n/a
21	chr3:112281021-112281071	CMK	blood:	n/a
22	chr3:112281021-112281071	T-47D	breast:	n/a
23	chr3:112281021-112281071	U87	brain:	n/a
24	chr3:112281021-112281071	NT2-D1	testis:	n/a
25	chr3:112281021-112281071	SAEC	small airway:	n/a
26	chr3:112281021-112281071	IMR90	lung:	fetal
27	chr3:112281021-112281071	HPAEpiC	pulmonary alveolar:	n/a
28	chr3:112281021-112281071	PFSK-1	brain:	n/a
29	chr3:112281021-112281071	AG09319	gingival:	n/a
30	chr3:112281021-112281071	H1-hESC	embryonic stem cell:	embryo
31	chr3:112281021-112281071	HCPEpiC	choroid plexus:	n/a
32	chr3:112281021-112281071	HAEpiC	amniotic membrane:	n/a
33	chr3:112281021-112281071	GM19239	blood:	n/a
34	chr3:112281021-112281071	PrEC	prostate:	n/a
35	chr3:112281021-112281071	NHBE	bronchial:	n/a
36	chr3:112281021-112281071	HCF	heart:	n/a
37	chr3:112281021-112281071	SK-N-SH	brain:	n/a
38	chr3:112281021-112281071	NB4	blood:	n/a
39	chr3:112281021-112281071	AoSMC	blood vessel:	n/a
40	chr3:112281021-112281071	BJ	skin:	n/a
41	chr3:112281021-112281071	Caco-2	colon:	n/a
42	chr3:112281021-112281071	MCF-7	breast:	n/a
43	chr3:112281021-112281071	ProgFib	skin:	n/a
44	chr3:112281021-112281071	HCM	heart:	n/a
45	chr3:112281021-112281071	SKMC	muscle:	n/a
46	chr3:112281021-112281071	HMEC	breast:	n/a
47	chr3:112281021-112281071	HIPEpiC	eye:	n/a
48	chr3:112281021-112281071	ovcar-3	ovarian:	n/a
49	chr3:112281021-112281071	K562	blood:	n/a
50	chr3:112281021-112281071	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:81790277..81790869-chr3:112280954..112281455,2	Hela-S3	cervix:
2	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
3	chr14:93673049..93673592-chr3:112280646..112281316,2	Hela-S3	cervix:
4	chr3:112279683..112282381-chr3:112710182..112712390,2	K562	blood:
5	chr3:111803332..111805315-chr3:112279253..112281220,2	MCF-7	breast:
6	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
7	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
8	chr3:112253490..112256363-chr3:112279039..112281187,3	K562	blood:
9	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
10	chr2:88315724..88316240-chr3:112280550..112281547,2	Hela-S3	cervix:
11	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
12	chr17:43394640..43395163-chr3:112280934..112281458,2	Hela-S3	cervix:
13	chr3:112280159..112284151-chr3:113775113..113778230,3	K562	blood:
14	chr3:111830456..111832040-chr3:112279153..112281688,2	K562	blood:
15	chr3:112280777..112282990-chr3:112288928..112291699,3	MCF-7	breast:
16	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
17	chr1:86046137..86047072-chr3:112280816..112281389,2	Hela-S3	cervix:
18	chr3:112257078..112259281-chr3:112279236..112282506,3	MCF-7	breast:

Variant related genes	Relation type
ATG3	TF binding region
SLC35A5	TF binding region
SLC35A5	CpG island
ATG3	CpG island
ENSG00000163608	Chromatin interaction
ENSG00000222724	Chromatin interaction
ENSG00000151576	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000163611	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000207940	Chromatin interaction
ENSG00000170270	Chromatin interaction
ENSG00000163617	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000114529	Chromatin interaction
ENSG00000012963	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]
rs72940078	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	chr3:112278200-112282000	Active TSS	K562	blood
2	chr3:112278200-112282200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:112278400-112282200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:112278600-112282400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:112278600-112283800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:112278800-112281600	Active TSS	Fetal Thymus	thymus
7	chr3:112278800-112281800	Active TSS	Thymus	Thymus
8	chr3:112278800-112282000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:112278800-112282000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr3:112278800-112282000	Active TSS	HSMM	muscle
11	chr3:112278800-112282200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:112278800-112282200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:112278800-112282200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:112278800-112282200	Active TSS	Psoas Muscle	Psoas
15	chr3:112279000-112282000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:112279000-112282000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:112279000-112282000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr3:112279000-112282000	Active TSS	Fetal Intestine Large	intestine
19	chr3:112279000-112282000	Active TSS	Fetal Intestine Small	intestine
20	chr3:112279000-112282000	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr3:112279000-112282000	Active TSS	GM12878-XiMat	blood
22	chr3:112279000-112282000	Active TSS	HMEC	breast
23	chr3:112279000-112282200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:112279000-112282200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr3:112279000-112282200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:112279000-112282200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:112279000-112282400	Active TSS	NHLF	lung
28	chr3:112279000-112282600	Active TSS	NHDF-Ad	bronchial
29	chr3:112279200-112281200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:112279200-112281600	Active TSS	Primary monocytes fromperipheralblood	blood
31	chr3:112279200-112281600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:112279200-112281800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:112279200-112281800	Active TSS	Fetal Muscle Leg	muscle
34	chr3:112279200-112281800	Active TSS	Fetal Stomach	stomach
35	chr3:112279200-112282000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:112279200-112282000	Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr3:112279200-112282000	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr3:112279200-112282200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:112279200-112282200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:112279200-112282200	Active TSS	Placenta	Placenta
41	chr3:112279200-112282200	Active TSS	Right Ventricle	heart
42	chr3:112279400-112281200	Active TSS	Primary T cells fromperipheralblood	blood
43	chr3:112279400-112281400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr3:112279400-112281800	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr3:112279400-112281800	Active TSS	HSMMtube	muscle
46	chr3:112279400-112282000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:112279400-112282000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:112279400-112282000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:112279400-112282000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:112279400-112282000	Active TSS	A549	lung

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