Variant report

Variant	rs889090
Chromosome Location	chr19:56004901-56004902
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	POLR2A	chr19:56004507-56005025	PFSK-1	brain:	n/a	n/a
2	MAZ	chr19:56003187-56006512	IMR90	lung:	n/a	chr19:56003287-56003296 chr19:56005653-56005662
3	POLR2A	chr19:56004749-56006349	U87	brain:	n/a	n/a
4	POLR2A	chr19:56004627-56006204	ProgFib	skin:	n/a	n/a
5	POLR2A	chr19:56004681-56006430	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55971480..55973183-chr19:56003027..56005168,2	K562	blood:
2	chr19:55996175..56001724-chr19:56002918..56007255,10	MCF-7	breast:
3	chr19:55970695..55974702-chr19:56000504..56005506,6	K562	blood:

Variant related genes	Relation type
SSC5D	TF binding region
ENSG00000179954	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000090971	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1559173	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2864436	0.80[CEU][hapmap]
rs929794	0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv912478	chr19:55936376-56045522	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	nsv912480	chr19:55972950-56009881	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv912481	chr19:55972950-56019597	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv912482	chr19:55972950-56062949	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
9	nsv912484	chr19:55977909-56019597	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv458833	chr19:55977909-56033088	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv580343	chr19:55977909-56033088	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv912485	chr19:55977909-56050844	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
14	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
15	nsv912490	chr19:55990975-56058737	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv912491	chr19:55990975-56062949	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv912492	chr19:55990975-56066163	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs889090	SSC5D	cis	lung	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56000200-56007800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:56000400-56005000	Enhancers	A549	lung
3	chr19:56000400-56005600	Bivalent Enhancer	Fetal Stomach	stomach
4	chr19:56000400-56009200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr19:56000600-56007000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:56001200-56005400	Weak transcription	K562	blood
7	chr19:56001200-56007600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:56001200-56015000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:56001200-56015200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:56002800-56005000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:56002800-56005800	Weak transcription	Lung	lung
12	chr19:56003600-56005200	Weak transcription	Spleen	Spleen
13	chr19:56003600-56005600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:56003800-56005200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:56003800-56005400	Weak transcription	Brain Anterior Caudate	brain
16	chr19:56004000-56005000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr19:56004200-56005000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr19:56004200-56008000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:56004400-56005000	Bivalent Enhancer	Colonic Mucosa	Colon
20	chr19:56004400-56005000	Enhancers	Fetal Heart	heart
21	chr19:56004400-56005000	Enhancers	Ovary	ovary
22	chr19:56004400-56005000	Enhancers	Right Ventricle	heart
23	chr19:56004400-56005200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:56004400-56005200	Flanking Active TSS	NHLF	lung
25	chr19:56004400-56005600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr19:56004400-56005600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:56004400-56005800	Enhancers	NH-A	brain
28	chr19:56004400-56006000	Bivalent Enhancer	Fetal Thymus	thymus
29	chr19:56004400-56006400	Active TSS	Fetal Kidney	kidney
30	chr19:56004400-56009400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:56004600-56005000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:56004600-56005000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
33	chr19:56004600-56005200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:56004600-56005200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:56004600-56005200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr19:56004600-56005200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr19:56004600-56005400	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr19:56004600-56005600	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:56004600-56005600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr19:56004600-56006000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr19:56004800-56005000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:56004800-56005000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:56004800-56005000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:56004800-56005000	Enhancers	Right Atrium	heart
45	chr19:56004800-56005200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:56004800-56005200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr19:56004800-56005600	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:56004800-56006000	Active TSS	Left Ventricle	heart
49	chr19:56004800-56006400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:56004800-56006400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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