Variant report

Variant	rs1107064
Chromosome Location	chr19:44669319-44669320
allele	A/G
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	SIN3AK20	chr19:44668804-44669628	A549	lung:	n/a	n/a
2	HEY1	chr19:44668646-44669550	HepG2	liver:	n/a	n/a
3	YY1	chr19:44668993-44669462	GM12878	blood:	n/a	chr19:44669266-44669274 chr19:44669263-44669285 chr19:44669262-44669274
4	MAX	chr19:44668811-44669671	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:44668648-44669553	HepG2	liver:	n/a	n/a
6	EP300	chr19:44668842-44669623	GM12878	blood:	n/a	chr19:44669166-44669173 chr19:44668988-44668995
7	POLR2A	chr19:44668859-44669656	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:44668802-44669436	HepG2	liver:	n/a	n/a
9	ZNF143	chr19:44668724-44669497	GM12878	blood:	n/a	chr19:44669190-44669209 chr19:44668991-44669000 chr19:44668914-44668933 chr19:44669049-44669058 chr19:44669128-44669137 chr19:44668915-44668930 chr19:44669116-44669135 chr19:44669121-44669139 chr19:44669195-44669213
10	ZBTB33	chr19:44668831-44669501	A549	lung:	n/a	n/a
11	MXI1	chr19:44668849-44669833	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:44668865-44669615	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr19:44668542-44669692	SK-N-SH	brain:	n/a	n/a
14	SPI1	chr19:44668715-44669533	HL-60	blood:	n/a	chr19:44668927-44668936
15	SP1	chr19:44668762-44669436	HepG2	liver:	n/a	n/a
16	YY1	chr19:44668933-44669473	HCT-116	colon:	n/a	chr19:44669266-44669274 chr19:44669263-44669285 chr19:44669262-44669274
17	MYC	chr19:44668791-44669514	NB4	blood:	n/a	n/a
18	TAF1	chr19:44668770-44669665	SK-N-SH	brain:	n/a	n/a
19	SIX5	chr19:44668920-44669444	H1-hESC	embryonic stem cell:	n/a	chr19:44669128-44669137 chr19:44668991-44669000 chr19:44669049-44669058
20	ELF1	chr19:44668752-44669536	K562	blood:	n/a	chr19:44669166-44669175 chr19:44668985-44668996 chr19:44669164-44669177 chr19:44669165-44669176 chr19:44668985-44668996
21	GABPA	chr19:44668863-44669393	HepG2	liver:	n/a	n/a
22	GTF2F1	chr19:44668986-44669426	H1-hESC	embryonic stem cell:	n/a	n/a
23	TAF1	chr19:44668919-44669433	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:44669162-44669372	A549	lung:	n/a	n/a
25	ATF1	chr19:44668848-44669410	K562	blood:	n/a	n/a
26	POLR2A	chr19:44668774-44669620	HUVEC	blood vessel:	n/a	n/a
27	E2F6	chr19:44668785-44669688	A549	lung:	n/a	chr19:44669471-44669481
28	GABPA	chr19:44668559-44669652	MCF-7	breast:	n/a	n/a
29	SP1	chr19:44668798-44669369	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr19:44668723-44669641	A549	lung:	n/a	n/a
31	ZMIZ1	chr19:44668895-44669387	K562	blood:	n/a	n/a
32	POLR2A	chr19:44668847-44670037	H1-neurons	neurons:	n/a	n/a
33	SPI1	chr19:44668819-44669408	GM12878	blood:	n/a	chr19:44668927-44668936
34	POLR2A	chr19:44668681-44669525	SK-N-MC	brain:	n/a	n/a
35	MAZ	chr19:44668782-44669438	K562	blood:	n/a	n/a
36	EP300	chr19:44668789-44669319	GM12878	blood:	n/a	chr19:44669166-44669173 chr19:44668988-44668995
37	REST	chr19:44668548-44669971	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr19:44668782-44669996	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:44668880-44669587	H1-hESC	embryonic stem cell:	n/a	n/a
40	RCOR1	chr19:44668887-44669476	HepG2	liver:	n/a	n/a
41	PML	chr19:44668753-44669733	GM12878	blood:	n/a	n/a
42	YY1	chr19:44668972-44669584	H1-hESC	embryonic stem cell:	n/a	chr19:44669266-44669274 chr19:44669263-44669285 chr19:44669474-44669485 chr19:44669262-44669274
43	POLR2A	chr19:44668898-44669491	K562	blood:	n/a	n/a
44	CUX1	chr19:44668715-44669472	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:44668805-44669522	ProgFib	skin:	n/a	n/a
46	THAP1	chr19:44669115-44669338	K562	blood:	n/a	n/a
47	TBP	chr19:44668763-44669431	Hela-S3	cervix:	n/a	n/a
48	STAT3	chr19:44668866-44669382	MCF10A-Er-Src	breast:	n/a	chr19:44669198-44669206 chr19:44669316-44669336 chr19:44668919-44668933 chr19:44669192-44669212 chr19:44668916-44668936 chr19:44669319-44669333 chr19:44669195-44669209 chr19:44668922-44668930
49	KAP1	chr19:44668650-44669598	U2OS	brain:	n/a	n/a
50	MAX	chr19:44668792-44669523	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44616225..44617902-chr19:44668355..44670566,2	MCF-7	breast:
2	chr19:44643597..44646401-chr19:44667704..44670290,3	K562	blood:
3	chr19:44643597..44647343-chr19:44667648..44671629,7	K562	blood:
4	chr19:44668036..44670553-chr19:44709491..44711796,2	MCF-7	breast:
5	chr19:44668674..44671221-chr19:44672001..44674509,3	K562	blood:
6	chr19:44644162..44647190-chr19:44667490..44670508,3	MCF-7	breast:
7	chr19:44669130..44670714-chr19:45003024..45005915,2	MCF-7	breast:

Variant related genes	Relation type
ZNF226	TF binding region
ENSG00000186019	Chromatin interaction
ENSG00000263002	Chromatin interaction
ENSG00000167380	Chromatin interaction
ENSG00000131115	Chromatin interaction
ENSG00000167384	Chromatin interaction
ENSG00000256294	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11667521	0.82[JPT][hapmap]
rs11671074	0.82[JPT][hapmap]
rs12461251	0.86[JPT][hapmap]
rs12609635	0.86[JPT][hapmap]
rs2051059	0.85[JPT][hapmap]
rs2125579	0.82[JPT][hapmap]
rs454904	0.82[ASW][hapmap]
rs4802218	0.85[JPT][hapmap]
rs7247369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8103838	0.82[JPT][hapmap]
rs8105073	0.86[JPT][hapmap]
rs8105479	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1107064	BLOC1S3	cis	parietal	SCAN
rs1107064	AP2A1	cis	parietal	SCAN
rs1107064	FPR2	cis	parietal	SCAN
rs1107064	SIGLEC11	cis	cerebellum	SCAN
rs1107064	TULP2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44667600-44669800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr19:44667800-44669800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:44668000-44669800	Active TSS	Rectal Smooth Muscle	rectum
4	chr19:44668400-44669600	Active TSS	Psoas Muscle	Psoas
5	chr19:44668400-44669600	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:44668400-44669800	Active TSS	Brain Hippocampus Middle	brain
7	chr19:44668400-44669800	Active TSS	Duodenum Mucosa	Duodenum
8	chr19:44668400-44669800	Active TSS	Right Atrium	heart
9	chr19:44668400-44669800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr19:44668400-44669800	Active TSS	K562	blood
11	chr19:44668400-44670000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:44668400-44670000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:44668400-44670000	Active TSS	Brain Cingulate Gyrus	brain
14	chr19:44668400-44670200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:44668400-44670400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:44668400-44670600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:44668400-44670800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:44668600-44669600	Active TSS	Primary T cells from cord blood	blood
19	chr19:44668600-44669600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:44668600-44669600	Active TSS	Brain Angular Gyrus	brain
21	chr19:44668600-44669600	Active TSS	Fetal Brain Female	brain
22	chr19:44668600-44669600	Active TSS	HUVEC	blood vessel
23	chr19:44668600-44669800	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:44668600-44669800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:44668600-44669800	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:44668600-44669800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:44668600-44669800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:44668600-44669800	Active TSS	Aorta	Aorta
29	chr19:44668600-44669800	Active TSS	Brain Anterior Caudate	brain
30	chr19:44668600-44669800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:44668600-44669800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr19:44668600-44669800	Active TSS	Placenta	Placenta
33	chr19:44668600-44669800	Active TSS	Fetal Thymus	thymus
34	chr19:44668600-44669800	Active TSS	Gastric	stomach
35	chr19:44668600-44669800	Active TSS	Pancreas	Pancrea
36	chr19:44668600-44669800	Active TSS	Small Intestine	intestine
37	chr19:44668600-44669800	Active TSS	Thymus	Thymus
38	chr19:44668600-44669800	Active TSS	HSMMtube	muscle
39	chr19:44668600-44669800	Active TSS	NHEK	skin
40	chr19:44668600-44670000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr19:44668600-44670000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr19:44668600-44670000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr19:44668600-44670000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:44668600-44670000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:44668600-44670000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:44668600-44670000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:44668600-44670000	Active TSS	Colonic Mucosa	Colon
48	chr19:44668600-44670000	Active TSS	Esophagus	oesophagus
49	chr19:44668600-44670000	Active TSS	Fetal Brain Male	brain
50	chr19:44668600-44670000	Active TSS	Fetal Kidney	kidney

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