Variant report

Variant	rs3888948
Chromosome Location	chr19:41285123-41285124
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	NR2F2	chr19:41283041-41285265	K562	blood:	n/a	n/a
2	MXI1	chr19:41282747-41285282	IMR90	lung:	n/a	n/a
3	MTA3	chr19:41282604-41285252	GM12878	blood:	n/a	n/a
4	MAFK	chr19:41283314-41285140	HepG2	liver:	n/a	n/a
5	FOSL2	chr19:41284802-41285211	HepG2	liver:	n/a	chr19:41285019-41285030
6	RFX5	chr19:41282710-41285139	HepG2	liver:	n/a	chr19:41283514-41283523 chr19:41283511-41283525 chr19:41283651-41283660 chr19:41283510-41283525
7	TAF1	chr19:41282964-41285167	H1-hESC	embryonic stem cell:	n/a	n/a
8	SP1	chr19:41282788-41285148	A549	lung:	n/a	chr19:41284001-41284013 chr19:41284602-41284611 chr19:41284139-41284151 chr19:41284383-41284392 chr19:41284360-41284369 chr19:41284381-41284393 chr19:41284378-41284392 chr19:41284052-41284064 chr19:41284359-41284371 chr19:41284002-41284016 chr19:41284382-41284392 chr19:41284601-41284611 chr19:41284864-41284878 chr19:41284002-41284012 chr19:41284799-41284813 chr19:41284383-41284392 chr19:41283866-41283875 chr19:41284003-41284012 chr19:41284053-41284062 chr19:41284356-41284370 chr19:41284007-41284014 chr19:41284002-41284011 chr19:41284382-41284391 chr19:41284600-41284612 chr19:41284600-41284612 chr19:41284052-41284064 chr19:41284602-41284611 chr19:41284361-41284370 chr19:41284002-41284012 chr19:41284053-41284067 chr19:41284001-41284012 chr19:41284601-41284611 chr19:41284181-41284195 chr19:41284001-41284013 chr19:41284136-41284150 chr19:41284360-41284370 chr19:41284140-41284149 chr19:41284359-41284371 chr19:41284381-41284393 chr19:41284139-41284151 chr19:41284597-41284611 chr19:41284382-41284392 chr19:41284002-41284011 chr19:41284054-41284063 chr19:41284601-41284610
9	SIX5	chr19:41282831-41285173	A549	lung:	n/a	chr19:41283617-41283626
10	CBX3	chr19:41284637-41285216	K562	blood:	n/a	n/a
11	MAX	chr19:41282804-41285428	A549	lung:	n/a	n/a
12	SP1	chr19:41282814-41285406	A549	lung:	n/a	chr19:41284001-41284013 chr19:41284602-41284611 chr19:41284139-41284151 chr19:41284383-41284392 chr19:41284360-41284369 chr19:41284381-41284393 chr19:41284378-41284392 chr19:41284052-41284064 chr19:41284359-41284371 chr19:41284002-41284016 chr19:41284382-41284392 chr19:41284601-41284611 chr19:41284864-41284878 chr19:41284002-41284012 chr19:41284799-41284813 chr19:41284383-41284392 chr19:41283866-41283875 chr19:41284003-41284012 chr19:41284053-41284062 chr19:41284356-41284370 chr19:41284007-41284014 chr19:41284002-41284011 chr19:41284382-41284391 chr19:41284600-41284612 chr19:41284600-41284612 chr19:41284052-41284064 chr19:41284602-41284611 chr19:41284361-41284370 chr19:41284002-41284012 chr19:41284053-41284067 chr19:41284001-41284012 chr19:41284601-41284611 chr19:41284181-41284195 chr19:41284001-41284013 chr19:41284136-41284150 chr19:41284360-41284370 chr19:41284140-41284149 chr19:41284359-41284371 chr19:41284381-41284393 chr19:41284139-41284151 chr19:41284597-41284611 chr19:41284382-41284392 chr19:41284002-41284011 chr19:41284054-41284063 chr19:41284601-41284610
13	RFX5	chr19:41282327-41285343	IMR90	lung:	n/a	chr19:41283514-41283523 chr19:41283511-41283525 chr19:41283651-41283660 chr19:41283510-41283525
14	RCOR1	chr19:41282984-41285191	HepG2	liver:	n/a	n/a
15	PBX3	chr19:41283516-41285212	SK-N-SH	brain:	n/a	chr19:41283827-41283836 chr19:41283651-41283660
16	SP1	chr19:41282909-41285140	H1-hESC	embryonic stem cell:	n/a	chr19:41284001-41284013 chr19:41284602-41284611 chr19:41284139-41284151 chr19:41284383-41284392 chr19:41284360-41284369 chr19:41284381-41284393 chr19:41284378-41284392 chr19:41284052-41284064 chr19:41284359-41284371 chr19:41284002-41284016 chr19:41284382-41284392 chr19:41284601-41284611 chr19:41284864-41284878 chr19:41284002-41284012 chr19:41284799-41284813 chr19:41284383-41284392 chr19:41283866-41283875 chr19:41284003-41284012 chr19:41284053-41284062 chr19:41284356-41284370 chr19:41284007-41284014 chr19:41284002-41284011 chr19:41284382-41284391 chr19:41284600-41284612 chr19:41284600-41284612 chr19:41284052-41284064 chr19:41284602-41284611 chr19:41284361-41284370 chr19:41284002-41284012 chr19:41284053-41284067 chr19:41284001-41284012 chr19:41284601-41284611 chr19:41284181-41284195 chr19:41284001-41284013 chr19:41284136-41284150 chr19:41284360-41284370 chr19:41284140-41284149 chr19:41284359-41284371 chr19:41284381-41284393 chr19:41284139-41284151 chr19:41284597-41284611 chr19:41284382-41284392 chr19:41284002-41284011 chr19:41284054-41284063 chr19:41284601-41284610
17	POLR2A	chr19:41282911-41285175	GM18505	blood:	n/a	n/a
18	FOSL2	chr19:41284791-41285279	HepG2	liver:	n/a	chr19:41285019-41285030
19	SIN3AK20	chr19:41283037-41285252	A549	lung:	n/a	n/a
20	FOSL2	chr19:41282975-41285315	A549	lung:	n/a	chr19:41285019-41285030 chr19:41283652-41283661
21	JUND	chr19:41284812-41285214	HepG2	liver:	n/a	chr19:41285020-41285031
22	BCL3	chr19:41282648-41285310	A549	lung:	n/a	chr19:41284233-41284246 chr19:41284824-41284833 chr19:41284149-41284158 chr19:41284141-41284150 chr19:41283403-41283412 chr19:41284234-41284247
23	ATF2	chr19:41284796-41285246	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr19:41282980-41285153	H1-hESC	embryonic stem cell:	n/a	n/a
25	RFX5	chr19:41282112-41285494	SK-N-SH	brain:	n/a	chr19:41283514-41283523 chr19:41283511-41283525 chr19:41283651-41283660 chr19:41283510-41283525
26	TCF12	chr19:41282710-41285318	A549	lung:	n/a	n/a
27	HCFC1	chr19:41282548-41285275	Hela-S3	cervix:	n/a	n/a
28	JUND	chr19:41283101-41285192	K562	blood:	n/a	chr19:41285020-41285031 chr19:41283652-41283661
29	FOS	chr19:41284746-41285228	HUVEC	blood vessel:	n/a	chr19:41285020-41285031
30	ARID3A	chr19:41284214-41285201	HepG2	liver:	n/a	n/a
31	MAZ	chr19:41283147-41285351	IMR90	lung:	n/a	n/a
32	REST	chr19:41282628-41285375	H1-neurons	neurons:	n/a	chr19:41283403-41283412

No.	Distal block	Cell Line	Cell type
1	chr19:41195540..41197710-chr19:41283825..41285603,2	MCF-7	breast:
2	chr19:41254354..41258983-chr19:41282435..41286100,11	MCF-7	breast:
3	chr19:41254259..41260312-chr19:41280225..41287427,15	K562	blood:
4	chr19:41280553..41283413-chr19:41284684..41288209,4	MCF-7	breast:
5	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
6	chr19:41220807..41223667-chr19:41282098..41285361,4	MCF-7	breast:
7	chr19:41282306..41285368-chr19:41311943..41315414,5	MCF-7	breast:
8	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
9	chr14:102505039..102506720-chr19:41282932..41285736,2	MCF-7	breast:
10	chr19:41282175..41285758-chr19:41311471..41315456,8	K562	blood:
11	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
12	chr19:41283422..41285801-chr19:41305183..41308009,2	MCF-7	breast:
13	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
14	chr19:41281732..41286442-chr19:41302482..41306628,13	K562	blood:
15	chr19:41283851..41288555-chr19:41290136..41292963,4	MCF-7	breast:
16	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
17	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:

Variant related genes	Relation type
RAB4B	TF binding region
RAB4B-EGLN2	TF binding region
ENSG00000197102	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12151282	1.00[YRI][hapmap]
rs7245595	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv13500	chr19:41283063-41285263	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	11 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	chr19:41282800-41285200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:41282800-41285400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41283000-41285200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr19:41283000-41285200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:41283000-41285200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:41283000-41285200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:41283000-41285400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:41283000-41285400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:41283000-41285400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:41283000-41285400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:41283200-41285200	Active TSS	HSMM	muscle
12	chr19:41283200-41285400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:41283200-41285400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr19:41283200-41285400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:41283200-41285400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:41283200-41285400	Active TSS	NHDF-Ad	bronchial
17	chr19:41283400-41285200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:41283400-41285400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr19:41284400-41285200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr19:41284400-41285200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:41284400-41285200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:41284400-41285200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr19:41284400-41285200	Flanking Active TSS	Liver	Liver
24	chr19:41284400-41285200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:41284400-41285200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr19:41284400-41285400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:41284600-41285200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr19:41284600-41285200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr19:41284600-41285200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr19:41284600-41285200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr19:41284600-41285200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr19:41284600-41285200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr19:41284600-41285200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:41284600-41285200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:41284600-41285200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:41284600-41285200	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr19:41284600-41285200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:41284600-41285200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:41284600-41285200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr19:41284600-41285200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr19:41284600-41285200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:41284600-41285200	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr19:41284600-41285200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr19:41284600-41285200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr19:41284600-41285200	Flanking Active TSS	Thymus	Thymus
46	chr19:41284600-41285200	Flanking Active TSS	HMEC	breast
47	chr19:41284600-41285200	Flanking Active TSS	HUVEC	blood vessel
48	chr19:41284600-41285400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr19:41284600-41285400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:41284600-41285400	Flanking Active TSS	Duodenum Mucosa	Duodenum

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