Variant report

Variant	rs6509096
Chromosome Location	chr19:44034346-44034347
allele	A/C
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	FOS	chr19:44033794-44034377	MCF10A-Er-Src	breast:	n/a	chr19:44033964-44033972 chr19:44033931-44033942 chr19:44033963-44033973 chr19:44033965-44033976 chr19:44033963-44033973 chr19:44033963-44033973 chr19:44033963-44033973

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44029247..44034379-chr19:44035166..44038879,9	MCF-7	breast:
2	chr19:44034271..44036948-chr19:44127770..44129771,2	K562	blood:

Variant related genes	Relation type
ZNF575	TF binding region
ETHE1	TF binding region
ENSG00000176472	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1125030	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs12978269	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs1799778	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2203990	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2256507	0.83[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2261316	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305375	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2355994	0.84[EUR][1000 genomes]
rs25486	0.88[JPT][hapmap]
rs25487	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2599435	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs2599440	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2599445	0.85[EUR][1000 genomes]
rs2599447	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2599454	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2599455	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2599456	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2599465	0.82[ASN][1000 genomes]
rs2682543	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2682549	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs2682553	0.84[EUR][1000 genomes]
rs2682559	0.82[ASN][1000 genomes]
rs2682566	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682578	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682579	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3810378	0.88[JPT][hapmap]
rs6509092	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7252955	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110232	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6509096	ZNF575	cis	lung	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44031600-44036600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:44031600-44036600	Weak transcription	Lung	lung
3	chr19:44031600-44036600	Weak transcription	Small Intestine	intestine
4	chr19:44031600-44036800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:44031600-44036800	Weak transcription	Spleen	Spleen
6	chr19:44031800-44034400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:44031800-44036600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:44031800-44036600	Weak transcription	Fetal Heart	heart
9	chr19:44031800-44036600	Weak transcription	HUVEC	blood vessel
10	chr19:44032000-44036400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:44032200-44034400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:44032200-44035800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr19:44032200-44036000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:44032200-44036000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:44032200-44036200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr19:44032200-44036200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr19:44032200-44036200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr19:44032200-44036200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:44032200-44036400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:44032200-44036400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:44032200-44036400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:44032200-44036400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:44032200-44036400	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:44032200-44036400	Weak transcription	Gastric	stomach
25	chr19:44032200-44036400	Weak transcription	Pancreas	Pancrea
26	chr19:44032200-44036400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr19:44032200-44036400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr19:44032200-44036400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr19:44032200-44036600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:44032200-44036600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:44032200-44036600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:44032200-44036600	Weak transcription	Adipose Nuclei	Adipose
33	chr19:44032200-44036600	Weak transcription	Aorta	Aorta
34	chr19:44032200-44036600	Weak transcription	Brain Germinal Matrix	brain
35	chr19:44032200-44036600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:44032200-44036600	Weak transcription	Esophagus	oesophagus
37	chr19:44032200-44036600	Weak transcription	Fetal Brain Male	brain
38	chr19:44032200-44036600	Weak transcription	Fetal Brain Female	brain
39	chr19:44032200-44036600	Weak transcription	Left Ventricle	heart
40	chr19:44032200-44036600	Weak transcription	Right Atrium	heart
41	chr19:44032200-44036600	Weak transcription	Right Ventricle	heart
42	chr19:44032200-44036600	Weak transcription	GM12878-XiMat	blood
43	chr19:44032200-44036800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:44032200-44036800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:44032200-44036800	Weak transcription	HSMM	muscle
46	chr19:44032400-44035000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:44032400-44036200	Weak transcription	Primary B cells from cord blood	blood
48	chr19:44032400-44036200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr19:44032400-44036200	Weak transcription	Liver	Liver
50	chr19:44032400-44036400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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