Variant report

Variant	rs3924057
Chromosome Location	chr3:142167042-142167043
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	RAD21	chr3:142166829-142167132	H1-hESC	embryonic stem cell:	n/a	n/a
2	NFATC1	chr3:142166664-142167464	GM12878	blood:	n/a	n/a
3	ZKSCAN1	chr3:142166610-142167188	Hela-S3	cervix:	n/a	n/a
4	YY1	chr3:142166734-142167140	H1-hESC	embryonic stem cell:	n/a	chr3:142166981-142166995
5	TCF12	chr3:142166761-142167143	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:142166467-142167381	U87	brain:	n/a	n/a
7	REST	chr3:142166776-142167122	PFSK-1	brain:	n/a	chr3:142166943-142166956
8	YY1	chr3:142166735-142167158	GM12891	blood:	n/a	chr3:142166981-142166995
9	TAF1	chr3:142166124-142167277	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP2	chr3:142166780-142167075	K562	blood:	n/a	chr3:142166946-142166961
11	FOXA1	chr3:142166683-142167097	T-47D	breast:	n/a	n/a
12	SMC3	chr3:142166523-142167245	Hela-S3	cervix:	n/a	n/a
13	PBX3	chr3:142166556-142167270	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr3:142166138-142167274	SK-N-MC	brain:	n/a	n/a
15	MAX	chr3:142166780-142167075	H1-hESC	embryonic stem cell:	n/a	n/a
16	USF1	chr3:142166756-142167182	A549	lung:	n/a	n/a
17	TAF1	chr3:142166574-142167194	K562	blood:	n/a	n/a
18	POLR2A	chr3:142166460-142167250	U87	brain:	n/a	n/a
19	TAF1	chr3:142166743-142167134	Hela-S3	cervix:	n/a	n/a
20	EP300	chr3:142166101-142167212	SK-N-SH	brain:	n/a	chr3:142166254-142166264 chr3:142167150-142167164
21	NR3C1	chr3:142166698-142167104	A549	lung:	n/a	n/a
22	POU2F2	chr3:142166766-142167094	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:142166171-142167184	GM10847	blood:	n/a	n/a
24	POLR2A	chr3:142166483-142167218	HUVEC	blood vessel:	n/a	n/a
25	E2F4	chr3:142166454-142167111	K562	blood:	n/a	n/a
26	POLR2A	chr3:142166431-142167307	MCF-7	breast:	n/a	n/a
27	HEY1	chr3:142166194-142167256	K562	blood:	n/a	chr3:142166225-142166240 chr3:142166981-142166996 chr3:142166979-142166994
28	POLR2A	chr3:142166141-142167191	K562	blood:	n/a	n/a
29	NFIC	chr3:142166629-142167224	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:142166235-142167196	MCF-7	breast:	n/a	n/a
31	E2F4	chr3:142166689-142167168	MCF10A-Er-Src	breast:	n/a	n/a
32	SP2	chr3:142166589-142167318	H1-hESC	embryonic stem cell:	n/a	chr3:142166946-142166961
33	POLR2A	chr3:142166310-142167246	GM12892	blood:	n/a	n/a
34	REST	chr3:142166533-142167308	A549	lung:	n/a	chr3:142166695-142166708 chr3:142166943-142166956
35	SIN3AK20	chr3:142165921-142167368	MCF-7	breast:	n/a	n/a
36	CHD2	chr3:142165959-142167457	Hela-S3	cervix:	n/a	n/a
37	BACH1	chr3:142166917-142167234	H1-hESC	embryonic stem cell:	n/a	n/a
38	TCF12	chr3:142166696-142167139	GM12878	blood:	n/a	n/a
39	CREB1	chr3:142166307-142167242	H1-hESC	embryonic stem cell:	n/a	n/a
40	GATA3	chr3:142166305-142167435	A549	lung:	n/a	n/a
41	MAX	chr3:142166685-142167232	SK-N-SH	brain:	n/a	n/a
42	TAF7	chr3:142166764-142167187	H1-hESC	embryonic stem cell:	n/a	n/a
43	SP2	chr3:142166590-142167295	HepG2	liver:	n/a	chr3:142166946-142166961
44	POLR2A	chr3:142165956-142167241	GM18951	blood:	n/a	n/a
45	CHD2	chr3:142165885-142167167	GM12878	blood:	n/a	n/a
46	MTA3	chr3:142166594-142167226	GM12878	blood:	n/a	n/a
47	USF2	chr3:142166781-142167065	H1-hESC	embryonic stem cell:	n/a	n/a
48	HEY1	chr3:142166552-142167282	HepG2	liver:	n/a	chr3:142166981-142166996 chr3:142166979-142166994
49	SRF	chr3:142166680-142167061	K562	blood:	n/a	chr3:142166908-142166918 chr3:142166950-142166960
50	POLR2A	chr3:142166593-142167209	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142164997..142168564-chr3:142170242..142173896,7	MCF-7	breast:
2	chr3:142166755..142169411-chr3:142174583..142176894,2	K562	blood:
3	chr3:142166774..142168881-chr3:142175818..142179023,4	MCF-7	breast:
4	chr3:142146723..142149402-chr3:142165233..142167666,2	K562	blood:
5	chr1:32479224..32479963-chr3:142166959..142167563,2	MCF-7	breast:
6	chr3:142165266..142167494-chr3:142176108..142178776,2	K562	blood:

Variant related genes	Relation type
XRN1	TF binding region
ENSG00000242479	TF binding region
ENSG00000121774	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000114127	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs34502778	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35582603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35978765	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55895932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56022646	1.00[EUR][1000 genomes]
rs56050554	1.00[EUR][1000 genomes]
rs57625476	1.00[EUR][1000 genomes]
rs59936227	1.00[EUR][1000 genomes]
rs6440101	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770411	1.00[EUR][1000 genomes]
rs6776083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6781412	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791858	1.00[EUR][1000 genomes]
rs6792428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7613884	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615480	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7620068	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621810	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7622266	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625306	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625764	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628677	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7632782	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7641297	0.94[LWK][hapmap]
rs7652760	1.00[EUR][1000 genomes]
rs7653387	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	51 gene(s)	inside rSNPs	diseases
3	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
7	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv528954	chr3:142164017-142219542	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr3:142163200-142167400	Active TSS	GM12878-XiMat	blood
2	chr3:142164400-142167600	Active TSS	Rectal Smooth Muscle	rectum
3	chr3:142164600-142167200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:142164600-142167600	Active TSS	Fetal Intestine Small	intestine
5	chr3:142164600-142167800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:142164800-142167200	Active TSS	Muscle Satellite Cultured Cells	--
7	chr3:142164800-142167400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:142164800-142167600	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr3:142164800-142167600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:142164800-142167600	Active TSS	Fetal Intestine Large	intestine
11	chr3:142164800-142167600	Active TSS	Ovary	ovary
12	chr3:142164800-142167600	Active TSS	HSMMtube	muscle
13	chr3:142164800-142167600	Active TSS	K562	blood
14	chr3:142164800-142167800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:142165000-142167200	Active TSS	HSMM	muscle
16	chr3:142165000-142167600	Active TSS	Right Ventricle	heart
17	chr3:142165000-142167600	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr3:142165000-142167600	Active TSS	NHDF-Ad	bronchial
19	chr3:142165000-142167800	Active TSS	Right Atrium	heart
20	chr3:142165000-142167800	Active TSS	NHLF	lung
21	chr3:142165200-142167200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:142165200-142167400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:142165200-142167400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:142165200-142167400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:142165200-142167400	Active TSS	Psoas Muscle	Psoas
26	chr3:142165200-142167600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:142165200-142167600	Active TSS	Primary T cells fromperipheralblood	blood
28	chr3:142165200-142167600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:142165200-142167600	Active TSS	Duodenum Mucosa	Duodenum
30	chr3:142165200-142167600	Active TSS	Thymus	Thymus
31	chr3:142165200-142167600	Active TSS	HMEC	breast
32	chr3:142165400-142167200	Active TSS	Liver	Liver
33	chr3:142165400-142167400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:142165400-142167400	Active TSS	Colonic Mucosa	Colon
35	chr3:142165400-142167400	Active TSS	Placenta	Placenta
36	chr3:142165400-142167400	Active TSS	A549	lung
37	chr3:142165400-142167600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:142165400-142167600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:142165400-142167600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:142165400-142167600	Active TSS	Fetal Muscle Leg	muscle
41	chr3:142165400-142167600	Active TSS	Fetal Thymus	thymus
42	chr3:142165400-142167600	Active TSS	Stomach Smooth Muscle	stomach
43	chr3:142165400-142167800	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr3:142165400-142167800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:142165600-142167200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:142165600-142167200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:142165600-142167200	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr3:142165600-142167200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:142165600-142167200	Bivalent/Poised TSS	HepG2	liver
50	chr3:142165600-142167400	Active TSS	Aorta	Aorta

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