Variant report

Variant	rs11878707
Chromosome Location	chr19:38811153-38811154
allele	C/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	MAX	chr19:38809841-38811231	A549	lung:	n/a	chr19:38810534-38810544
2	CTCF	chr19:38811020-38811170	A549	lung:	n/a	n/a
3	E2F6	chr19:38810350-38811213	A549	lung:	n/a	chr19:38810533-38810542 chr19:38810416-38810425
4	E2F6	chr19:38810132-38811203	H1-hESC	embryonic stem cell:	n/a	chr19:38810533-38810542 chr19:38810416-38810425

No.	Distal block	Cell Line	Cell type
1	chr19:38810024..38812525-chr19:38892478..38895075,3	MCF-7	breast:
2	chr19:38810865..38812439-chr19:38865172..38866719,2	MCF-7	breast:
3	chr19:38713590..38716581-chr19:38810078..38812613,2	MCF-7	breast:
4	chr19:38757716..38759532-chr19:38810909..38812505,2	MCF-7	breast:
5	chr19:38810007..38812286-chr19:38825422..38828123,4	MCF-7	breast:
6	chr19:38753833..38757251-chr19:38808796..38812283,9	MCF-7	breast:

Variant related genes	Relation type
YIF1B	TF binding region
ENSG00000167642	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1060455	1.00[GIH][hapmap]
rs12460599	0.82[AFR][1000 genomes]
rs17640544	1.00[TSI][hapmap]
rs2072350	1.00[GIH][hapmap]
rs2074979	1.00[GIH][hapmap]
rs2286550	0.82[CHB][hapmap];1.00[GIH][hapmap]
rs2286551	1.00[GIH][hapmap]
rs2302226	1.00[GIH][hapmap]
rs34614180	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35077481	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35323359	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35710536	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3745960	1.00[GIH][hapmap]
rs3745962	1.00[GIH][hapmap]
rs3859550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71354996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7253827	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38809200-38811400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:38809200-38813200	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr19:38809400-38811400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:38809600-38811200	Flanking Active TSS	Colonic Mucosa	Colon
5	chr19:38809600-38811200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38809600-38811400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38809800-38811200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
8	chr19:38809800-38811200	Flanking Active TSS	HUVEC	blood vessel
9	chr19:38809800-38811400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:38809800-38811400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:38809800-38811400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:38809800-38811400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr19:38809800-38811600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:38809800-38811600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr19:38809800-38811800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:38809800-38811800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:38809800-38812000	Active TSS	Aorta	Aorta
18	chr19:38809800-38812600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr19:38809800-38813200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:38810000-38811200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr19:38810000-38811200	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr19:38810000-38811200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:38810000-38811200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:38810000-38811200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:38810000-38811400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr19:38810000-38811400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
27	chr19:38810000-38811400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
28	chr19:38810000-38811600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr19:38810000-38811800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr19:38810200-38811200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:38810200-38811200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:38810200-38811200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:38810200-38811200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
34	chr19:38810200-38811200	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr19:38810200-38811400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr19:38810200-38811400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr19:38810200-38811400	Flanking Active TSS	Liver	Liver
38	chr19:38810200-38811400	Active TSS	Esophagus	oesophagus
39	chr19:38810200-38811400	Active TSS	Lung	lung
40	chr19:38810200-38811600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr19:38810200-38811600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:38810200-38811800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:38810200-38811800	Active TSS	Colon Smooth Muscle	Colon
44	chr19:38810200-38811800	Active TSS	Gastric	stomach
45	chr19:38810200-38811800	Active TSS	Small Intestine	intestine
46	chr19:38810200-38812000	Active TSS	Ovary	ovary
47	chr19:38810400-38811200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:38810400-38811200	Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr19:38810400-38811200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:38810400-38811200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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