Variant report

Variant	rs2279856
Chromosome Location	chr3:143692018-143692019
allele	C/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	POLR2A	chr3:143689636-143692179	H1-hESC	embryonic stem cell:	n/a	n/a
2	HDAC2	chr3:143689898-143692374	MCF-7	breast:	n/a	chr3:143690819-143690828 chr3:143690369-143690383
3	POLR2A	chr3:143689448-143692708	HUVEC	blood vessel:	n/a	n/a
4	ZBTB7A	chr3:143691366-143692190	ECC-1	luminal epithelium:	n/a	chr3:143691964-143691971
5	CTCF	chr3:143692000-143692150	GM12870	blood:	n/a	n/a
6	GTF2F1	chr3:143691373-143692836	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:143689953-143692471	GM12891	blood:	n/a	n/a
8	YY1	chr3:143691121-143692109	HepG2	liver:	n/a	chr3:143691907-143691921
9	POLR2A	chr3:143689718-143692074	HEK293	kidney:	n/a	n/a
10	CTCF	chr3:143691947-143692185	HepG2	liver:	n/a	n/a
11	CTCF	chr3:143691881-143692257	T-47D	breast:	n/a	n/a
12	CTCF	chr3:143691955-143692224	GM12878	blood:	n/a	n/a
13	BATF	chr3:143691917-143692241	GM12878	blood:	n/a	n/a
14	TCF7L2	chr3:143689631-143692487	HCT-116	colon:	n/a	n/a
15	TBL1XR1	chr3:143691415-143692306	K562	blood:	n/a	n/a
16	CTCF	chr3:143691998-143692165	Kidney_OC	kidney:	n/a	n/a
17	ZBTB7A	chr3:143691336-143692202	ECC-1	luminal epithelium:	n/a	chr3:143691964-143691971
18	CTCF	chr3:143692000-143692150	Caco-2	colon:	n/a	n/a
19	MAX	chr3:143689475-143692453	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
20	POLR2A	chr3:143689516-143692415	HL-60	blood:	n/a	n/a
21	MAX	chr3:143689667-143692276	ECC-1	luminal epithelium:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
22	FOXP2	chr3:143691827-143692218	SK-N-MC	brain:	n/a	n/a
23	MYC	chr3:143691908-143692231	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F6	chr3:143690710-143692133	H1-hESC	embryonic stem cell:	n/a	chr3:143690818-143690827 chr3:143690784-143690794 chr3:143691005-143691017
25	MYC	chr3:143689557-143692334	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
26	KAP1	chr3:143690666-143692802	HEK293	kidney:	n/a	n/a
27	POLR2A	chr3:143689882-143692298	MCF-7	breast:	n/a	n/a
28	FOXM1	chr3:143689578-143692479	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:143689635-143692573	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:143691928-143692513	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr3:143691957-143692797	MCF10A-Er-Src	breast:	n/a	n/a
32	MAX	chr3:143689459-143692886	Hela-S3	cervix:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
33	POLR2A	chr3:143691958-143692463	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr3:143689651-143692557	GM18526	blood:	n/a	n/a
35	MYC	chr3:143689633-143692296	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
36	MAX	chr3:143689528-143692416	HCT-116	colon:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
37	YY1	chr3:143691919-143692252	K562	blood:	n/a	n/a
38	CTCF	chr3:143692000-143692150	SAEC	small airway:	n/a	n/a
39	MTA3	chr3:143691891-143692557	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:143691928-143692645	K562	blood:	n/a	n/a
41	CTCF	chr3:143692000-143692150	HUVEC	blood vessel:	n/a	n/a
42	PML	chr3:143691834-143692273	K562	blood:	n/a	n/a
43	POLR2A	chr3:143689670-143692495	GM15510	blood:	n/a	n/a
44	CTCF	chr3:143692000-143692150	HCM	heart:	n/a	n/a
45	MXI1	chr3:143689654-143692425	GM12878	blood:	n/a	chr3:143689823-143689838 chr3:143689811-143689826
46	POLR2A	chr3:143689898-143692254	MCF-7	breast:	n/a	n/a
47	RUNX3	chr3:143689706-143692538	GM12878	blood:	n/a	chr3:143690436-143690445 chr3:143690436-143690445 chr3:143690482-143690497
48	MXI1	chr3:143689589-143692923	Hela-S3	cervix:	n/a	chr3:143689823-143689838 chr3:143689811-143689826 chr3:143689595-143689604
49	CTCF	chr3:143692000-143692150	WERI-Rb-1	eye:	n/a	n/a
50	MYC	chr3:143689554-143692333	NB4	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:143692006-143692056	HRE	kidney:	n/a
2	chr3:143692006-143692056	BJ	skin:	n/a
3	chr3:143692006-143692056	HRCEpiC	kidney:	n/a
4	chr3:143692006-143692056	Jurkat	blood:	n/a
5	chr3:143692006-143692056	T-47D	breast:	n/a
6	chr3:143692006-143692056	AoSMC	blood vessel:	n/a
7	chr3:143692006-143692056	HL-60	blood:	n/a
8	chr3:143692006-143692056	GM12891	blood:	n/a
9	chr3:143692006-143692056	HIPEpiC	eye:	n/a
10	chr3:143692006-143692056	Hela-S3	cervix:	n/a
11	chr3:143692006-143692056	PANC-1	pancreas:	n/a
12	chr3:143692006-143692056	AG04450	lung:	fetal
13	chr3:143692006-143692056	HEK293	kidney:	embryo
14	chr3:143692006-143692056	H1-hESC	embryonic stem cell:	embryo
15	chr3:143692006-143692056	HPAEpiC	pulmonary alveolar:	n/a
16	chr3:143692006-143692056	AG09319	gingival:	n/a
17	chr3:143692006-143692056	HRPEpiC	eye:	n/a
18	chr3:143692006-143692056	AG10803	skin:	n/a
19	chr3:143692006-143692056	A549	lung:	n/a
20	chr3:143692006-143692056	ECC-1	luminal epithelium:	n/a
21	chr3:143692006-143692056	NHDF-neo	bronchial:	n/a
22	chr3:143692006-143692056	AG04449	skin:	fetal
23	chr3:143692006-143692056	NH-A	brain:	n/a
24	chr3:143692006-143692056	ovcar-3	ovarian:	n/a
25	chr3:143692006-143692056	HEEpiC	esophagus:	n/a
26	chr3:143692006-143692056	ProgFib	skin:	n/a
27	chr3:143692006-143692056	AG09309	skin:	n/a
28	chr3:143692006-143692056	GM19239	blood:	n/a
29	chr3:143692006-143692056	HMEC	breast:	n/a
30	chr3:143692006-143692056	HCF	heart:	n/a
31	chr3:143692006-143692056	MCF10A-Er-Src	breast:	n/a
32	chr3:143692006-143692056	SK-N-SH_RA	brain:	n/a
33	chr3:143692006-143692056	PrEC	prostate:	n/a
34	chr3:143692006-143692056	NB4	blood:	n/a
35	chr3:143692006-143692056	HUVEC	blood vessel:	n/a
36	chr3:143692006-143692056	LNCaP	prostate:	n/a
37	chr3:143692006-143692056	HCM	heart:	n/a
38	chr3:143692006-143692056	RPTEC	kidney:	n/a
39	chr3:143692006-143692056	NT2-D1	testis:	n/a
40	chr3:143692006-143692056	HepG2	liver:	n/a
41	chr3:143692006-143692056	Hepatocyte	liver:	n/a
42	chr3:143692006-143692056	K562	blood:	n/a
43	chr3:143692006-143692056	HNPCEpiC	eye:	n/a
44	chr3:143692006-143692056	HCPEpiC	choroid plexus:	n/a
45	chr3:143692006-143692056	SK-N-MC	brain:	n/a
46	chr3:143692006-143692056	SK-N-SH	brain:	n/a
47	chr3:143692006-143692056	CMK	blood:	n/a
48	chr3:143692006-143692056	GM06990	blood:	n/a
49	chr3:143692006-143692056	HAEpiC	amniotic membrane:	n/a
50	chr3:143692006-143692056	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:17097769..17100478-chr3:143690055..143692307,2	MCF-7	breast:
2	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:
3	chr16:88876624..88878169-chr3:143691035..143693133,2	MCF-7	breast:

Variant related genes	Relation type
C3orf58	TF binding region
C3orf58	CpG island
ENSG00000110700	Chromatin interaction
ENSG00000181804	Chromatin interaction
ENSG00000198931	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10513234	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10513235	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13064130	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13078840	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs13081286	0.85[CEU][hapmap]
rs1466941	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs17602500	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17667256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1979910	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1992093	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34038325	0.91[ASN][1000 genomes]
rs34071449	0.87[ASN][1000 genomes]
rs34402874	0.86[ASN][1000 genomes]
rs35072578	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35211123	0.92[ASN][1000 genomes]
rs35362423	0.91[ASN][1000 genomes]
rs35692092	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35716467	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35877644	0.83[ASN][1000 genomes]
rs4315684	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4446205	0.90[ASN][1000 genomes]
rs4535221	0.86[ASN][1000 genomes]
rs4563409	0.92[ASN][1000 genomes]
rs59287916	0.86[ASN][1000 genomes]
rs60505453	0.93[ASN][1000 genomes]
rs62267390	0.93[ASN][1000 genomes]
rs6440210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6767811	0.81[CEU][hapmap]
rs6768153	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs721572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs723491	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7610378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7634145	0.85[CEU][hapmap]
rs9683376	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 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	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143693200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:143689000-143694400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143689200-143693200	Active TSS	A549	lung
7	chr3:143689200-143693400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:143689200-143693800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:143689200-143694400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:143689200-143695400	Active TSS	K562	blood
11	chr3:143689200-143695800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
13	chr3:143689400-143692400	Active TSS	Primary T cells from cord blood	blood
14	chr3:143689400-143692400	Active TSS	Duodenum Mucosa	Duodenum
15	chr3:143689400-143692600	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr3:143689400-143693000	Active TSS	Fetal Kidney	kidney
17	chr3:143689400-143693200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr3:143689400-143693200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:143689400-143693200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:143689400-143693200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:143689400-143693200	Active TSS	Stomach Mucosa	stomach
22	chr3:143689400-143693400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:143689400-143693400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:143689400-143693400	Active TSS	Colon Smooth Muscle	Colon
25	chr3:143689400-143693400	Active TSS	Psoas Muscle	Psoas
26	chr3:143689400-143693400	Active TSS	Right Ventricle	heart
27	chr3:143689400-143693600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:143689400-143693600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr3:143689400-143693600	Active TSS	Fetal Muscle Trunk	muscle
30	chr3:143689400-143693600	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:143689400-143693600	Active TSS	Thymus	Thymus
32	chr3:143689400-143693600	Active TSS	NHDF-Ad	bronchial
33	chr3:143689400-143693800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:143689400-143693800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:143689400-143694000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:143689400-143694000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:143689400-143694000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr3:143689400-143694000	Active TSS	Fetal Thymus	thymus
39	chr3:143689400-143694200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:143689400-143694200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr3:143689400-143694200	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr3:143689400-143694400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr3:143689400-143694400	Active TSS	Fetal Muscle Leg	muscle
44	chr3:143689400-143694800	Active TSS	Brain Anterior Caudate	brain
45	chr3:143689400-143695000	Active TSS	Brain Hippocampus Middle	brain
46	chr3:143689400-143695000	Active TSS	Fetal Brain Male	brain
47	chr3:143689400-143695000	Active TSS	Fetal Intestine Large	intestine
48	chr3:143689400-143695200	Active TSS	NHLF	lung
49	chr3:143689400-143695400	Active TSS	Brain Cingulate Gyrus	brain
50	chr3:143689400-143695400	Active TSS	Right Atrium	heart

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