Variant report

Variant	rs3875144
Chromosome Location	chr19:41285377-41285378
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	MAX	chr19:41282804-41285428	A549	lung:	n/a	n/a
2	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
3	RFX5	chr19:41282112-41285494	SK-N-SH	brain:	n/a	chr19:41283514-41283523 chr19:41283511-41283525 chr19:41283651-41283660 chr19:41283510-41283525
4	POLR2A	chr19:41285340-41285539	K562	blood:	n/a	n/a

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	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
7	chr14:102505039..102506720-chr19:41282932..41285736,2	MCF-7	breast:
8	chr19:41282175..41285758-chr19:41311471..41315456,8	K562	blood:
9	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
10	chr19:41283422..41285801-chr19:41305183..41308009,2	MCF-7	breast:
11	chr19:41253800..41258892-chr19:41281807..41286457,14	MCF-7	breast:
12	chr19:41281732..41286442-chr19:41302482..41306628,13	K562	blood:
13	chr19:41283851..41288555-chr19:41290136..41292963,4	MCF-7	breast:
14	chr19:41254259..41259402-chr19:41281476..41286314,17	K562	blood:
15	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10403040	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10405596	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10405633	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411008	0.97[EUR][1000 genomes]
rs10413760	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10416308	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10425480	0.89[AFR][1000 genomes]
rs17713068	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2233152	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287692	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28660501	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56101381	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41282800-41285400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41283000-41285400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:41283000-41285400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:41283000-41285400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:41283000-41285400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:41283200-41285400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:41283200-41285400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:41283200-41285400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:41283200-41285400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:41283200-41285400	Active TSS	NHDF-Ad	bronchial
11	chr19:41283400-41285400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:41284400-41285400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:41284600-41285400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr19:41284600-41285400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:41284600-41285400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr19:41284600-41285400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
17	chr19:41284600-41285400	Flanking Active TSS	Hela-S3	cervix
18	chr19:41284600-41285400	Flanking Active TSS	Osteobl	bone
19	chr19:41284600-41285600	Flanking Active TSS	Dnd41	blood
20	chr19:41284600-41286000	Enhancers	Spleen	Spleen
21	chr19:41284800-41285400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:41284800-41285400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:41284800-41285400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:41284800-41285400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:41284800-41285400	Flanking Active TSS	A549	lung
26	chr19:41284800-41285400	Flanking Active TSS	HepG2	liver
27	chr19:41284800-41286400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:41285000-41285400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:41285000-41285400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:41285000-41285400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr19:41285000-41285400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:41285000-41285400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:41285000-41285400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr19:41285000-41285400	Enhancers	Primary hematopoietic stem cells	blood
35	chr19:41285000-41285400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr19:41285000-41285400	Enhancers	Colon Smooth Muscle	Colon
37	chr19:41285000-41285400	Enhancers	Fetal Heart	heart
38	chr19:41285000-41285400	Enhancers	Fetal Intestine Large	intestine
39	chr19:41285000-41285400	Enhancers	Fetal Intestine Small	intestine
40	chr19:41285000-41285400	Enhancers	Right Ventricle	heart
41	chr19:41285000-41285400	Enhancers	Stomach Mucosa	stomach
42	chr19:41285000-41285400	Flanking Active TSS	GM12878-XiMat	blood
43	chr19:41285000-41285600	Enhancers	Fetal Thymus	thymus
44	chr19:41285000-41285800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr19:41285000-41285800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:41285000-41286000	Enhancers	Placenta	Placenta
47	chr19:41285000-41286000	Weak transcription	Lung	lung
48	chr19:41285000-41286200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:41285000-41286200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr19:41285000-41286600	Genic enhancers	Primary B cells from peripheral blood	blood

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