Variant report

Variant	rs204554
Chromosome Location	chr19:44932323-44932324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44927888..44930648-chr19:44931223..44933120,2	MCF-7	breast:
2	chr19:44931433..44933674-chr19:44935471..44937509,2	K562	blood:
3	chr19:44932216..44933778-chr19:44935937..44937487,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1734622	1.00[ASN][1000 genomes]
rs1865385	1.00[ASN][1000 genomes]
rs204527	1.00[ASN][1000 genomes]
rs204529	1.00[ASN][1000 genomes]
rs204530	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204532	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204542	1.00[ASN][1000 genomes]
rs204548	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs204550	1.00[ASN][1000 genomes]
rs204553	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs204556	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571041	1.00[ASN][1000 genomes]
rs2571053	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2571059	1.00[ASN][1000 genomes]
rs2686756	1.00[ASN][1000 genomes]
rs2686757	1.00[ASN][1000 genomes]
rs2686769	1.00[ASN][1000 genomes]
rs431273	1.00[ASN][1000 genomes]
rs62118147	1.00[ASN][1000 genomes]
rs629579	1.00[ASN][1000 genomes]
rs8107008	1.00[CHB][hapmap]
rs930462	1.00[CHB][hapmap]
rs954314	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515911	chr19:44852134-44935019	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1062330	chr19:44863939-44938277	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2763206	chr19:44885379-44941728	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3318557	chr19:44892181-44938875	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3318558	chr19:44892356-44938748	Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv9734	chr19:44892761-44940023	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2756827	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv2758764	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1059267	chr19:44896386-44938277	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1055870	chr19:44896386-44938779	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2421963	chr19:44896398-44938791	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv442465	chr19:44896398-44938791	ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1058295	chr19:44896888-44938779	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1065703	chr19:44898759-44938779	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1065424	chr19:44899546-44938779	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv817849	chr19:44903015-44935019	ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv16323	chr19:44928244-44938721	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv579857	chr19:44928885-44935019	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs204554	PGLYRP1	cis	cerebellum	SCAN
rs204554	IL4I1	cis	parietal	SCAN
rs204554	EXOC3L2	cis	parietal	SCAN
rs204554	CCDC155	cis	parietal	SCAN
rs204554	NOVA2	cis	parietal	SCAN
rs204554	RCN3	cis	cerebellum	SCAN
rs204554	PGLYRP1	cis	parietal	SCAN
rs204554	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44926200-44932400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:44928000-44943600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:44928200-44941000	ZNF genes & repeats	Liver	Liver
4	chr19:44928200-44941000	ZNF genes & repeats	Ovary	ovary
5	chr19:44928200-44943400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:44929200-44945400	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:44929400-44941000	ZNF genes & repeats	Fetal Brain Female	brain
9	chr19:44931400-44932400	Weak transcription	Aorta	Aorta
10	chr19:44931800-44932600	ZNF genes & repeats	Psoas Muscle	Psoas
11	chr19:44931800-44934400	ZNF genes & repeats	Fetal Heart	heart
12	chr19:44931800-44940200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:44931800-44941000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr19:44931800-44941600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:44932000-44934600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
16	chr19:44932000-44934800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:44932000-44936400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr19:44932000-44936800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
19	chr19:44932000-44938800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr19:44932000-44939800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr19:44932000-44940000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:44932000-44941000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
23	chr19:44932000-44943400	ZNF genes & repeats	Fetal Lung	lung
24	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr19:44932200-44933800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:44932200-44936000	ZNF genes & repeats	Fetal Kidney	kidney
27	chr19:44932200-44936600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:44932200-44936600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
29	chr19:44932200-44937400	ZNF genes & repeats	Fetal Brain Male	brain
30	chr19:44932200-44937800	ZNF genes & repeats	HSMMtube	muscle
31	chr19:44932200-44940200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:44932200-44940400	ZNF genes & repeats	Brain Hippocampus Middle	brain
33	chr19:44932200-44940800	ZNF genes & repeats	Colon Smooth Muscle	Colon
34	chr19:44932200-44941000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:44932200-44941000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr19:44932200-44941000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:44932200-44941000	ZNF genes & repeats	Left Ventricle	heart
38	chr19:44932200-44943400	ZNF genes & repeats	A549	lung
39	chr19:44932200-44943600	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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