Variant report

Variant	rs12485273
Chromosome Location	chr3:139253871-139253872
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	GATA3	chr3:139253777-139254128	T-47D	breast:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
2	RAD21	chr3:139253713-139254263	SK-N-SH_RA	brain:	n/a	n/a
3	GATA2	chr3:139252419-139254559	SH-SY5Y	brain:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253969-139253978
4	EP300	chr3:139252506-139253883	ECC-1	luminal epithelium:	n/a	chr3:139253631-139253641
5	TCF12	chr3:139252972-139254172	SK-N-SH	brain:	n/a	n/a
6	EP300	chr3:139252994-139254143	Hela-S3	cervix:	n/a	chr3:139253631-139253641
7	REST	chr3:139253845-139254221	SK-N-SH	brain:	n/a	n/a
8	GTF2F1	chr3:139253086-139254253	Hela-S3	cervix:	n/a	n/a
9	MAX	chr3:139252417-139253901	HCT-116	colon:	n/a	n/a
10	MAX	chr3:139252974-139254272	Hela-S3	cervix:	n/a	chr3:139253978-139253987
11	GATA3	chr3:139253624-139254250	MCF-7	breast:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
12	MYC	chr3:139253214-139254085	MCF10A-Er-Src	breast:	n/a	chr3:139253978-139253987
13	ZNF263	chr3:139252619-139254885	HEK293-T-REx	kidney:	n/a	chr3:139254383-139254404
14	SMC3	chr3:139252744-139254281	Hela-S3	cervix:	n/a	n/a
15	MAX	chr3:139252796-139254283	Hela-S3	cervix:	n/a	chr3:139253978-139253987
16	EP300	chr3:139251629-139259175	SK-N-SH	brain:	n/a	chr3:139256357-139256366 chr3:139253631-139253641 chr3:139252024-139252040 chr3:139256356-139256365
17	GATA3	chr3:139252835-139254318	SK-N-SH	brain:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
18	EP300	chr3:139253734-139254473	SK-N-SH_RA	brain:	n/a	n/a
19	JUND	chr3:139252502-139254257	HCT-116	colon:	n/a	n/a
20	CEBPB	chr3:139253241-139254017	IMR90	lung:	n/a	n/a
21	EP300	chr3:139252410-139254345	SK-N-SH_RA	brain:	n/a	chr3:139253631-139253641
22	GATA3	chr3:139253760-139254138	T-47D	breast:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
23	RCOR1	chr3:139252942-139254300	Hela-S3	cervix:	n/a	n/a
24	KAP1	chr3:139252592-139254801	HEK293	kidney:	n/a	n/a
25	EGR1	chr3:139252436-139254155	HCT-116	colon:	n/a	chr3:139253297-139253321 chr3:139252809-139252822 chr3:139252810-139252820 chr3:139252810-139252819 chr3:139252809-139252822 chr3:139252804-139252826
26	TCF7L2	chr3:139252539-139254255	Hela-S3	cervix:	n/a	n/a
27	RCOR1	chr3:139253846-139254135	K562	blood:	n/a	n/a
28	SP1	chr3:139252416-139253939	HCT-116	colon:	n/a	chr3:139252721-139252733 chr3:139252632-139252644 chr3:139252636-139252650
29	TCF12	chr3:139252593-139254418	SK-N-SH	brain:	n/a	chr3:139252841-139252849
30	KAP1	chr3:139252751-139254431	U2OS	brain:	n/a	n/a
31	GATA3	chr3:139252760-139254379	MCF-7	breast:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
32	POLR2A	chr3:139253089-139254169	Hela-S3	cervix:	n/a	n/a
33	TBP	chr3:139253019-139254220	Hela-S3	cervix:	n/a	n/a
34	TFAP2C	chr3:139253055-139254253	Hela-S3	cervix:	n/a	n/a
35	GATA3	chr3:139253532-139254274	SH-SY5Y	brain:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
36	CEBPB	chr3:139252973-139254191	Hela-S3	cervix:	n/a	n/a
37	NFIC	chr3:139252882-139254265	SK-N-SH	brain:	n/a	n/a
38	GATA3	chr3:139252453-139254414	SK-N-SH	brain:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
39	POLR2A	chr3:139252526-139254282	HCT-116	colon:	n/a	n/a
40	CEBPB	chr3:139252516-139253995	HCT-116	colon:	n/a	n/a
41	GATA3	chr3:139253788-139254236	MCF-7	breast:	n/a	chr3:139253969-139253979 chr3:139253966-139253982 chr3:139253971-139253978 chr3:139253970-139253978 chr3:139253969-139253978
42	NFIC	chr3:139252285-139253872	ECC-1	luminal epithelium:	n/a	chr3:139252460-139252477
43	RFX5	chr3:139253798-139254245	Hela-S3	cervix:	n/a	chr3:139253977-139253992 chr3:139253977-139253992
44	POLR2A	chr3:139252929-139254291	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:139253838-139253888	Hepatocyte	liver:	n/a
2	chr3:139253838-139253888	HCM	heart:	n/a
3	chr3:139253838-139253888	MCF-7	breast:	n/a
4	chr3:139253838-139253888	GM12878	blood:	n/a
5	chr3:139253838-139253888	HNPCEpiC	eye:	n/a
6	chr3:139253838-139253888	ProgFib	skin:	n/a
7	chr3:139253838-139253888	HCT-116	colon:	n/a
8	chr3:139253838-139253888	Jurkat	blood:	n/a
9	chr3:139253838-139253888	SKMC	muscle:	n/a
10	chr3:139253838-139253888	MCF10A-Er-Src	breast:	n/a
11	chr3:139253838-139253888	HRCEpiC	kidney:	n/a
12	chr3:139253838-139253888	IMR90	lung:	fetal
13	chr3:139253838-139253888	HCPEpiC	choroid plexus:	n/a
14	chr3:139253838-139253888	A549	lung:	n/a
15	chr3:139253838-139253888	HEEpiC	esophagus:	n/a
16	chr3:139253838-139253888	NB4	blood:	n/a
17	chr3:139253838-139253888	HRPEpiC	eye:	n/a
18	chr3:139253838-139253888	PrEC	prostate:	n/a
19	chr3:139253838-139253888	Hela-S3	cervix:	n/a
20	chr3:139253838-139253888	PANC-1	pancreas:	n/a
21	chr3:139253838-139253888	AG04450	lung:	fetal
22	chr3:139253838-139253888	HepG2	liver:	n/a
23	chr3:139253838-139253888	HAEpiC	amniotic membrane:	n/a
24	chr3:139253838-139253888	HCF	heart:	n/a
25	chr3:139253838-139253888	AoSMC	blood vessel:	n/a
26	chr3:139253838-139253888	BJ	skin:	n/a
27	chr3:139253838-139253888	HPAEpiC	pulmonary alveolar:	n/a
28	chr3:139253838-139253888	GM12892	blood:	n/a
29	chr3:139253838-139253888	HEK293	kidney:	embryo
30	chr3:139253838-139253888	T-47D	breast:	n/a
31	chr3:139253838-139253888	NT2-D1	testis:	n/a
32	chr3:139253838-139253888	GM19239	blood:	n/a
33	chr3:139253838-139253888	HL-60	blood:	n/a
34	chr3:139253838-139253888	ECC-1	luminal epithelium:	n/a
35	chr3:139253838-139253888	K562	blood:	n/a
36	chr3:139253838-139253888	ovcar-3	ovarian:	n/a
37	chr3:139253838-139253888	RPTEC	kidney:	n/a
38	chr3:139253838-139253888	CMK	blood:	n/a
39	chr3:139253838-139253888	HRE	kidney:	n/a
40	chr3:139253838-139253888	NHDF-neo	bronchial:	n/a
41	chr3:139253838-139253888	AG09319	gingival:	n/a
42	chr3:139253838-139253888	SK-N-SH_RA	brain:	n/a
43	chr3:139253838-139253888	LNCaP	prostate:	n/a
44	chr3:139253838-139253888	HUVEC	blood vessel:	n/a
45	chr3:139253838-139253888	PFSK-1	brain:	n/a
46	chr3:139253838-139253888	HMEC	breast:	n/a
47	chr3:139253838-139253888	SK-N-MC	brain:	n/a
48	chr3:139253838-139253888	U87	brain:	n/a
49	chr3:139253838-139253888	Caco-2	colon:	n/a
50	chr3:139253838-139253888	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139252110..139254375-chr3:139256957..139258581,2	MCF-7	breast:
2	chr3:139253381..139256319-chr3:139269568..139271702,2	MCF-7	breast:
3	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:
4	chr3:139252531..139254445-chr3:139267067..139268675,2	MCF-7	breast:
5	chr3:139239944..139241919-chr3:139253042..139255747,2	MCF-7	breast:
6	chr3:139245782..139250222-chr3:139250781..139254846,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248932	TF binding region
ENSG00000248932	CpG island
ENSG00000114115	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12493507	0.85[CEU][hapmap];0.83[CHD][hapmap]
rs1511570	0.85[CEU][hapmap]
rs2071387	0.82[ASW][hapmap];0.87[CEU][hapmap];0.88[LWK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3772868	0.85[CEU][hapmap]
rs4407373	0.84[CEU][hapmap]
rs4683502	0.85[CEU][hapmap]
rs893703	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12485273	RBP1	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139249600-139254400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:139249600-139255000	Enhancers	Pancreas	Pancrea
3	chr3:139249600-139256400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:139249800-139257400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:139250000-139256600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:139250200-139255000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:139250200-139255000	Enhancers	Brain Anterior Caudate	brain
8	chr3:139250600-139254600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:139250600-139254600	Enhancers	Fetal Lung	lung
10	chr3:139250600-139255400	Enhancers	Brain Angular Gyrus	brain
11	chr3:139250600-139256800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:139250800-139254400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:139250800-139257400	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:139251000-139254600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:139251000-139255800	Enhancers	Fetal Kidney	kidney
16	chr3:139251200-139254200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:139251200-139254400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:139251200-139254600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:139251200-139254600	Enhancers	Fetal Intestine Large	intestine
20	chr3:139251200-139255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:139251200-139257400	Genic enhancers	Fetal Intestine Small	intestine
22	chr3:139251400-139254200	Enhancers	HepG2	liver
23	chr3:139251400-139255400	Enhancers	Placenta	Placenta
24	chr3:139251400-139256400	Enhancers	Liver	Liver
25	chr3:139251400-139257200	Enhancers	Duodenum Mucosa	Duodenum
26	chr3:139251600-139254600	Enhancers	Fetal Muscle Leg	muscle
27	chr3:139251600-139255800	Enhancers	Fetal Brain Male	brain
28	chr3:139251600-139256400	Enhancers	HMEC	breast
29	chr3:139251800-139254400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:139251800-139254600	Enhancers	Fetal Muscle Trunk	muscle
31	chr3:139251800-139255200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:139251800-139258600	Enhancers	Fetal Heart	heart
33	chr3:139252000-139254600	Flanking Active TSS	NH-A	brain
34	chr3:139252000-139254800	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr3:139252000-139254800	Enhancers	Fetal Brain Female	brain
36	chr3:139252000-139257600	Enhancers	Left Ventricle	heart
37	chr3:139252200-139257600	Enhancers	Brain Substantia Nigra	brain
38	chr3:139252400-139254800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:139252400-139256200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:139252600-139254200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:139252600-139254200	Flanking Active TSS	Hela-S3	cervix
42	chr3:139252600-139254400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr3:139252600-139254400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:139252600-139254400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:139252600-139254800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:139252600-139254800	Enhancers	Esophagus	oesophagus
47	chr3:139252600-139254800	Enhancers	K562	blood
48	chr3:139252600-139255000	Enhancers	Fetal Thymus	thymus
49	chr3:139252600-139255000	Enhancers	HSMM	muscle
50	chr3:139252600-139255200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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