Variant report

Variant	rs4802841
Chromosome Location	chr19:52201763-52201764
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	chr19:52201460-52202290	U87	brain:	n/a	n/a
2	POLR2A	chr19:52201622-52201820	K562	blood:	n/a	n/a
3	POLR2A	chr19:52201647-52202167	SK-N-MC	brain:	n/a	n/a
4	FOS	chr19:52201664-52201865	MCF10A-Er-Src	breast:	n/a	chr19:52201718-52201726 chr19:52201719-52201726 chr19:52201714-52201725 chr19:52201718-52201727
5	POLR2A	chr19:52201231-52202290	U87	brain:	n/a	n/a
6	POLR2A	chr19:52201754-52201875	A549	lung:	n/a	n/a
7	FOS	chr19:52201602-52201820	MCF10A-Er-Src	breast:	n/a	chr19:52201718-52201726 chr19:52201719-52201726 chr19:52201714-52201725 chr19:52201718-52201727
8	FOS	chr19:52201603-52201864	MCF10A-Er-Src	breast:	n/a	chr19:52201718-52201726 chr19:52201719-52201726 chr19:52201714-52201725 chr19:52201718-52201727
9	POLR2A	chr19:52200929-52202092	MCF-7	breast:	n/a	n/a
10	FOS	chr19:52201602-52201825	MCF10A-Er-Src	breast:	n/a	chr19:52201718-52201726 chr19:52201719-52201726 chr19:52201714-52201725 chr19:52201718-52201727
11	POLR2A	chr19:52200881-52203018	A549	lung:	n/a	n/a
12	POLR2A	chr19:52199636-52204065	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:52201723-52201791	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52195958..52197871-chr19:52199159..52203308,3	MCF-7	breast:
2	chr19:52200661..52202641-chr19:52206213..52209050,2	K562	blood:
3	chr19:52198700..52202637-chr19:52203349..52207450,6	K562	blood:
4	chr19:52199590..52202022-chr19:52311266..52313737,2	MCF-7	breast:
5	chr19:52193714..52195914-chr19:52201685..52203516,2	K562	blood:

Variant related genes	Relation type
SPACA6P	TF binding region
ENSG00000269959	Chromatin interaction
ENSG00000182310	Chromatin interaction
ENSG00000198972	Chromatin interaction
ENSG00000273318	Chromatin interaction
ENSG00000207550	Chromatin interaction
ENSG00000208008	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11881781	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167417	1.00[ASN][1000 genomes]
rs2167418	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs2864920	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs2864922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs34764077	1.00[ASN][1000 genomes]
rs35627212	0.82[EUR][1000 genomes]
rs35653323	1.00[ASN][1000 genomes]
rs73054871	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106727	0.84[EUR][1000 genomes]
rs8107937	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109852	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic 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 miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4802841	ZNF587	cis	cerebellum	SCAN
rs4802841	ZNF784	cis	parietal	SCAN
rs4802841	ZNF304	cis	parietal	SCAN
rs4802841	SLC27A5	cis	parietal	SCAN
rs4802841	CNOT3	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52194200-52205400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52194600-52205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:52194600-52207000	Weak transcription	Psoas Muscle	Psoas
4	chr19:52194800-52204600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:52194800-52205200	Weak transcription	Stomach Mucosa	stomach
6	chr19:52195000-52205600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:52195000-52205600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
11	chr19:52195400-52204600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
13	chr19:52195600-52203200	Strong transcription	Fetal Intestine Small	intestine
14	chr19:52195600-52204600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:52195600-52204800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr19:52195800-52204600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:52196200-52204800	Weak transcription	Colonic Mucosa	Colon
18	chr19:52196200-52204800	Strong transcription	NHEK	skin
19	chr19:52196200-52205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:52196200-52205600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:52196400-52202800	Strong transcription	Fetal Intestine Large	intestine
22	chr19:52196400-52203000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:52196400-52203000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:52196400-52203200	Strong transcription	NHLF	lung
25	chr19:52196400-52204600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr19:52196400-52204600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:52196400-52205200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:52196400-52206400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:52196400-52206600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr19:52196600-52202600	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr19:52196600-52203000	Strong transcription	NHDF-Ad	bronchial
32	chr19:52196600-52204600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:52196600-52205200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:52196600-52205200	Strong transcription	Adipose Nuclei	Adipose
35	chr19:52196600-52205800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:52196800-52202400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:52196800-52205000	Strong transcription	Brain Germinal Matrix	brain
38	chr19:52196800-52205400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:52197000-52204600	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr19:52197000-52204800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:52197000-52204800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:52197000-52205200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:52197000-52205600	Strong transcription	Fetal Lung	lung
44	chr19:52197000-52205800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:52197200-52204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:52197200-52204800	Strong transcription	HMEC	breast
47	chr19:52197400-52202200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:52197400-52203000	Strong transcription	Brain Angular Gyrus	brain
49	chr19:52197600-52203000	Strong transcription	HSMMtube	muscle
50	chr19:52197600-52205400	Strong transcription	Fetal Stomach	stomach

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