Variant report

Variant	rs2270196
Chromosome Location	chr19:44506623-44506624
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	RCOR1	chr19:44506440-44507367	K562	blood:	n/a	n/a
2	POLR2A	chr19:44506381-44507453	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr19:44506522-44507300	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr19:44506580-44507603	MCF-7	breast:	n/a	n/a
5	GABPA	chr19:44506410-44507830	A549	lung:	n/a	chr19:44507267-44507276
6	POLR2A	chr19:44506474-44507683	PBDE	blood:	n/a	n/a
7	CHD1	chr19:44506605-44507528	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:44506194-44507446	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:44506482-44507410	HUVEC	blood vessel:	n/a	n/a
10	TEAD4	chr19:44506582-44507321	K562	blood:	n/a	n/a
11	POLR2A	chr19:44506596-44507954	GM12892	blood:	n/a	n/a
12	NFIC	chr19:44506591-44507447	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr19:44506342-44507587	A549	lung:	n/a	n/a
14	POLR2A	chr19:44506211-44507620	HepG2	liver:	n/a	n/a
15	SP1	chr19:44506550-44507356	A549	lung:	n/a	chr19:44507266-44507278 chr19:44507267-44507276 chr19:44507268-44507277 chr19:44507263-44507277 chr19:44507268-44507277
16	MTA3	chr19:44506529-44508278	GM12878	blood:	n/a	n/a
17	MXI1	chr19:44506290-44508318	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr19:44506525-44507455	U87	brain:	n/a	n/a
19	POLR2A	chr19:44506566-44507314	MCF10A-Er-Src	breast:	n/a	n/a
20	HCFC1	chr19:44506552-44507485	K562	blood:	n/a	n/a
21	SIN3A	chr19:44506546-44507737	H1-hESC	embryonic stem cell:	n/a	chr19:44507319-44507332
22	UBTF	chr19:44506562-44506662	K562	blood:	n/a	n/a
23	GABPA	chr19:44506415-44507534	MCF-7	breast:	n/a	chr19:44507267-44507276
24	POLR2A	chr19:44506613-44507168	HUVEC	blood vessel:	n/a	n/a
25	TAF1	chr19:44506603-44507313	A549	lung:	n/a	n/a
26	TEAD4	chr19:44506552-44507305	HepG2	liver:	n/a	n/a
27	ELF1	chr19:44506564-44507574	HCT-116	colon:	n/a	chr19:44507099-44507110 chr19:44507099-44507110
28	GATA2	chr19:44506440-44507544	SH-SY5Y	brain:	n/a	n/a
29	MAX	chr19:44506535-44507202	K562	blood:	n/a	n/a
30	ETS1	chr19:44506469-44507541	A549	lung:	n/a	chr19:44507098-44507111 chr19:44507099-44507108 chr19:44507265-44507276 chr19:44507099-44507108 chr19:44507099-44507108 chr19:44507097-44507107 chr19:44507099-44507108 chr19:44507099-44507108 chr19:44507099-44507108 chr19:44507097-44507108 chr19:44507099-44507108 chr19:44507096-44507112 chr19:44507063-44507076 chr19:44506992-44507005 chr19:44506993-44507006
31	POLR2A	chr19:44506613-44507430	HL-60	blood:	n/a	n/a
32	ZBTB33	chr19:44506491-44507310	A549	lung:	n/a	n/a
33	REST	chr19:44506552-44507348	A549	lung:	n/a	n/a
34	ZNF263	chr19:44506057-44508044	HEK293-T-REx	kidney:	n/a	n/a
35	GATA3	chr19:44506535-44506816	SH-SY5Y	brain:	n/a	n/a
36	POLR2A	chr19:44506620-44507333	U87	brain:	n/a	n/a
37	TCF12	chr19:44506543-44507403	A549	lung:	n/a	n/a
38	REST	chr19:44506620-44507092	PFSK-1	brain:	n/a	n/a
39	MXI1	chr19:44506569-44507283	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr19:44506589-44507559	HL-60	blood:	n/a	n/a
41	RFX5	chr19:44506606-44507498	HepG2	liver:	n/a	n/a
42	REST	chr19:44506452-44507408	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr19:44506611-44507414	HUVEC	blood vessel:	n/a	n/a
44	BCLAF1	chr19:44506601-44507305	GM12878	blood:	n/a	chr19:44507099-44507108
45	HNF4G	chr19:44506605-44507618	HepG2	liver:	n/a	n/a
46	ELF1	chr19:44506530-44507531	HCT-116	colon:	n/a	chr19:44507099-44507110 chr19:44507099-44507110
47	YY1	chr19:44506392-44507489	SK-N-SH	brain:	n/a	chr19:44507267-44507276
48	POLR2A	chr19:44506525-44507450	U87	brain:	n/a	n/a
49	TBL1XR1	chr19:44506599-44507238	K562	blood:	n/a	n/a
50	ELF1	chr19:44506555-44507564	MCF-7	breast:	n/a	chr19:44507099-44507110 chr19:44507099-44507110

No.	Distal block	Cell Line	Cell type
1	chr19:44493777..44495330-chr19:44504111..44506690,2	K562	blood:
2	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:
3	chr19:44506046..44508713-chr19:44597601..44599146,2	MCF-7	breast:
4	chr19:44506534..44508269-chr19:44616199..44620011,3	K562	blood:
5	chr19:44505664..44508645-chr19:44527908..44530282,2	MCF-7	breast:
6	chr19:44487658..44489792-chr19:44505545..44508358,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF45-2	chr19:44506417-44506985	ENSG00000266921.1

Variant related genes	Relation type
ZNF230	TF binding region
ENSG00000267680	Chromatin interaction
ENSG00000204920	Chromatin interaction
ENSG00000186019	Chromatin interaction
ENSG00000267022	Chromatin interaction
ENSG00000267144	Chromatin interaction
ENSG00000256294	Chromatin interaction
ENSG00000159885	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10418363	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083732	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083733	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881151	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12232810	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996408	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2191566	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35292176	0.89[EUR][1000 genomes]
rs367209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367499	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377503	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810406	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs384544	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803667	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803669	0.84[ASN][1000 genomes]
rs4803675	0.86[JPT][hapmap]
rs55703004	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101767	0.93[EUR][1000 genomes]
rs56171514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317065	0.82[ASN][1000 genomes]
rs59963278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115482	0.80[ASN][1000 genomes]
rs62119173	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62119176	0.87[ASN][1000 genomes]
rs6509133	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509138	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7245749	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252394	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253205	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254261	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7255145	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255315	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255512	0.85[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs7256908	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258517	0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73037629	0.80[ASN][1000 genomes]
rs8104605	0.86[JPT][hapmap]
rs8105571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2270196	OPA3	cis	cerebellum	SCAN
rs2270196	ZNF155	cis	multi-tissue	Pritchard
rs2270196	FOXA3	cis	cerebellum	SCAN
rs2270196	OPA3	cis	parietal	SCAN
rs2270196	PTGIR	cis	cerebellum	SCAN
rs2270196	HIF3A	cis	parietal	SCAN
rs2270196	CCDC114	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44506000-44506800	Flanking Active TSS	Dnd41	blood
2	chr19:44506000-44508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44506200-44506800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:44506200-44506800	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr19:44506200-44506800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:44506200-44506800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr19:44506200-44506800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:44506200-44506800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr19:44506200-44506800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:44506200-44506800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:44506200-44506800	Flanking Active TSS	Liver	Liver
12	chr19:44506200-44506800	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr19:44506200-44506800	Flanking Active TSS	Fetal Brain Male	brain
14	chr19:44506200-44506800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr19:44506200-44506800	Flanking Active TSS	HepG2	liver
16	chr19:44506200-44506800	Flanking Active TSS	NHEK	skin
17	chr19:44506200-44507000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:44506200-44507000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:44506200-44507200	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:44506200-44507600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr19:44506200-44507600	Active TSS	Fetal Brain Female	brain
22	chr19:44506200-44507600	Active TSS	NH-A	brain
23	chr19:44506200-44507800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:44506200-44507800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:44506200-44507800	Active TSS	Right Atrium	heart
26	chr19:44506200-44507800	Active TSS	Stomach Mucosa	stomach
27	chr19:44506200-44508000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:44506200-44508000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:44506200-44508000	Active TSS	Psoas Muscle	Psoas
30	chr19:44506200-44508000	Active TSS	Right Ventricle	heart
31	chr19:44506200-44508000	Active TSS	HSMMtube	muscle
32	chr19:44506200-44508200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr19:44506200-44508200	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:44506200-44508200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr19:44506200-44508400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:44506200-44508400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr19:44506200-44508400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:44506200-44508400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr19:44506200-44508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:44506200-44508400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:44506400-44506800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr19:44506400-44506800	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr19:44506400-44506800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr19:44506400-44506800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr19:44506400-44506800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:44506400-44506800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:44506400-44506800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:44506400-44506800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:44506400-44506800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr19:44506400-44506800	Flanking Active TSS	Brain Angular Gyrus	brain

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