Variant report

Variant	rs3974625
Chromosome Location	chr4:103737557-103737558
allele	A/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	TCF12	chr4:103736900-103737766	SK-N-SH	brain:	n/a	n/a
2	JUND	chr4:103737032-103737662	SK-N-SH	brain:	n/a	n/a
3	EP300	chr4:103737031-103737638	SK-N-SH	brain:	n/a	chr4:103737208-103737222 chr4:103737041-103737055 chr4:103737297-103737306
4	POLR2A	chr4:103737147-103737638	PFSK-1	brain:	n/a	n/a
5	YY1	chr4:103736967-103737656	SK-N-SH	brain:	n/a	n/a
6	JUND	chr4:103737015-103737676	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:103737021-103737694	U87	brain:	n/a	n/a
8	GATA3	chr4:103736966-103737646	SK-N-SH	brain:	n/a	chr4:103737016-103737037 chr4:103737585-103737592
9	POLR2A	chr4:103737011-103737566	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr4:103737026-103737645	SK-N-SH	brain:	n/a	n/a
11	YY1	chr4:103737006-103737624	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr4:103736948-103737655	SK-N-SH	brain:	n/a	n/a
13	USF1	chr4:103737042-103737678	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr4:103736987-103737664	U87	brain:	n/a	n/a
15	POLR2A	chr4:103737218-103737733	GM12892	blood:	n/a	n/a
16	JUND	chr4:103737177-103737564	HepG2	liver:	n/a	n/a
17	CEBPB	chr4:103737028-103737626	IMR90	lung:	n/a	chr4:103737371-103737383
18	TBL1XR1	chr4:103737476-103737676	K562	blood:	n/a	n/a
19	POLR2A	chr4:103736655-103737626	HepG2	liver:	n/a	n/a
20	MYC	chr4:103737205-103737652	MCF10A-Er-Src	breast:	n/a	chr4:103737319-103737328
21	ARID3A	chr4:103737396-103737590	HepG2	liver:	n/a	n/a
22	MAFK	chr4:103737108-103737562	IMR90	lung:	n/a	n/a
23	PBX3	chr4:103737006-103737712	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr4:103737089-103737694	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:103737097-103737626	K562	blood:	n/a	n/a
26	USF2	chr4:103737414-103737572	K562	blood:	n/a	n/a
27	FOSL2	chr4:103737117-103737612	SK-N-SH	brain:	n/a	n/a
28	USF1	chr4:103737104-103737630	HCT-116	colon:	n/a	n/a
29	TCF12	chr4:103737005-103737717	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr4:103737021-103737632	U87	brain:	n/a	n/a
31	POLR2A	chr4:103736624-103740163	K562	blood:	n/a	n/a
32	USF1	chr4:103737035-103737597	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr4:103737448-103737618	HepG2	liver:	n/a	n/a
34	USF1	chr4:103737117-103737584	ECC-1	luminal epithelium:	n/a	n/a
35	MYC	chr4:103737501-103737573	MCF10A-Er-Src	breast:	n/a	n/a
36	GATA3	chr4:103736955-103737641	SK-N-SH	brain:	n/a	chr4:103737016-103737037 chr4:103737585-103737592
37	FOS	chr4:103737126-103737609	MCF10A-Er-Src	breast:	n/a	chr4:103737285-103737296 chr4:103737367-103737378

No.	Distal block	Cell Line	Cell type
1	chr4:103719443..103722708-chr4:103736970..103739381,3	K562	blood:
2	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:
3	chr4:103736438..103740967-chr4:103789693..103792681,4	K562	blood:
4	chr4:103715909..103718007-chr4:103736247..103738557,2	MCF-7	breast:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000238948	Chromatin interaction
ENSG00000145354	Chromatin interaction
ENSG00000109332	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17033248	1.00[CEU][hapmap]
rs17033351	1.00[CEU][hapmap]
rs6811212	1.00[CEU][hapmap]
rs6827148	1.00[CEU][hapmap]
rs6847207	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7668564	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7670621	1.00[CEU][hapmap]
rs7670680	1.00[CEU][hapmap]
rs7677366	1.00[CEU][hapmap]
rs7677599	1.00[CEU][hapmap]
rs7690706	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7698383	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7699703	1.00[CEU][hapmap]
rs9307278	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
2	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
4	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
5	chr4:103724400-103745800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:103725000-103740600	Weak transcription	Fetal Brain Female	brain
7	chr4:103725600-103745000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:103726800-103738600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:103728400-103744400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:103730000-103740600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:103731200-103737800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:103731400-103740600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:103731800-103739000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:103732000-103739600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:103732600-103738000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr4:103732600-103744400	Weak transcription	Brain Germinal Matrix	brain
17	chr4:103732800-103739200	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:103732800-103740000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:103732800-103745000	Weak transcription	Lung	lung
20	chr4:103732800-103746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:103732800-103746400	Weak transcription	Esophagus	oesophagus
22	chr4:103733000-103741600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:103733400-103741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:103733400-103743200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:103733800-103738400	Weak transcription	Right Ventricle	heart
26	chr4:103734000-103738200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:103734600-103737600	Strong transcription	Fetal Lung	lung
28	chr4:103734600-103745600	Weak transcription	Fetal Stomach	stomach
29	chr4:103734800-103737600	Weak transcription	HepG2	liver
30	chr4:103734800-103738600	Weak transcription	Placenta	Placenta
31	chr4:103734800-103744800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:103735400-103739600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:103735400-103740800	Weak transcription	Fetal Kidney	kidney
34	chr4:103735600-103746200	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr4:103735800-103739200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr4:103735800-103740800	Genic enhancers	NHDF-Ad	bronchial
37	chr4:103735800-103741800	Enhancers	Small Intestine	intestine
38	chr4:103736000-103738000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:103736000-103738200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:103736000-103739000	Weak transcription	Left Ventricle	heart
41	chr4:103736000-103739200	Enhancers	Liver	Liver
42	chr4:103736000-103746600	Weak transcription	Pancreas	Pancrea
43	chr4:103736400-103737800	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr4:103736400-103738000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:103736400-103739200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:103736400-103739600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:103736400-103740200	Enhancers	Brain Substantia Nigra	brain
48	chr4:103736600-103737800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:103736600-103738200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr4:103736600-103738400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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