Variant report

Variant	rs2965190
Chromosome Location	chr19:19451591-19451592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19451447-19451860	K562	blood:	n/a	n/a
2	POLR2A	chr19:19451575-19454057	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:19451555-19451679	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:19451363-19454957	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:19451458-19454871	K562	blood:	n/a	n/a
6	POLR2A	chr19:19451517-19454929	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:19451498-19451842	GM12891	blood:	n/a	n/a
8	POLR2A	chr19:19451476-19451856	K562	blood:	n/a	n/a
9	POLR2A	chr19:19451524-19451700	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:19451573-19454644	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19451384..19453641-chr19:19459438..19462508,3	K562	blood:
2	chr19:19445427..19448842-chr19:19450344..19454175,4	MCF-7	breast:
3	chr19:19445107..19449445-chr19:19450274..19452019,4	K562	blood:
4	chr19:19431266..19434636-chr19:19448982..19451713,3	MCF-7	breast:

No data

Variant related genes	Relation type
MAU2	TF binding region
ENSG00000129933	Chromatin interaction
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1005372	1.00[CHD][hapmap]
rs10406278	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10419684	1.00[CHD][hapmap]
rs1064389	1.00[CHD][hapmap]
rs1064395	0.90[TSI][hapmap]
rs11085264	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs11555053	0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11669730	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs11670775	0.83[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs11670882	0.90[TSI][hapmap]
rs1529745	0.80[AMR][1000 genomes]
rs1557723	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1560687	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs16996127	0.83[CEU][hapmap];0.93[TSI][hapmap]
rs17216041	0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17684164	0.82[CEU][hapmap]
rs17751061	0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1989867	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2010506	0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2011503	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2060274	0.83[CEU][hapmap]
rs2060275	0.83[CEU][hapmap]
rs2074302	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2228601	1.00[CHD][hapmap]
rs2315023	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2315282	0.81[EUR][1000 genomes]
rs2860494	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2905422	0.80[EUR][1000 genomes]
rs2905429	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905433	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2905434	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2916070	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2916072	0.82[AMR][1000 genomes]
rs2965178	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2965179	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965181	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965184	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2965186	0.82[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965195	0.93[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965201	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34487417	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35854118	0.82[EUR][1000 genomes]
rs4239639	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808206	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs4808934	0.90[TSI][hapmap]
rs4808944	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808951	0.83[CEU][hapmap]
rs4808962	0.93[CEU][hapmap]
rs4808968	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs55762233	0.82[EUR][1000 genomes]
rs55765017	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55822665	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56044734	0.82[EUR][1000 genomes]
rs56135441	0.82[EUR][1000 genomes]
rs56144632	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56212061	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56278919	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56291054	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57436187	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511027	0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6511029	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7250233	0.83[CEU][hapmap];0.91[GIH][hapmap]
rs72999059	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72999063	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72999068	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs751857	0.92[GIH][hapmap];0.81[TSI][hapmap]
rs754256	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap]
rs756997	0.83[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs756999	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8100097	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8101219	0.88[GIH][hapmap]
rs8105642	0.83[CEU][hapmap]
rs8110171	0.83[CEU][hapmap]
rs8110250	0.83[CEU][hapmap]
rs8111093	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs998732	0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2965190	DDX49	cis	cerebellum	SCAN
rs2965190	JUND	cis	parietal	SCAN
rs2965190	IL12RB1	cis	parietal	SCAN
rs2965190	LSM4	cis	cerebellum	SCAN
rs2965190	OCEL1	cis	parietal	SCAN
rs2965190	GATAD2A	cis	parietal	SCAN
rs2965190	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs2965190	YJEFN3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19433200-19452800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:19433400-19469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:19433400-19470600	Strong transcription	Fetal Stomach	stomach
4	chr19:19433800-19468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:19433800-19469800	Strong transcription	Fetal Intestine Large	intestine
6	chr19:19433800-19470400	Strong transcription	Placenta	Placenta
7	chr19:19434200-19469000	Strong transcription	Fetal Thymus	thymus
8	chr19:19434200-19469800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:19434200-19469800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:19434600-19466000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:19434800-19470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:19435000-19471000	Strong transcription	Fetal Brain Female	brain
13	chr19:19435400-19453400	Strong transcription	Stomach Smooth Muscle	stomach
14	chr19:19435600-19455400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:19435600-19468600	Strong transcription	Dnd41	blood
16	chr19:19435600-19470400	Strong transcription	Brain Germinal Matrix	brain
17	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
18	chr19:19436000-19460600	Strong transcription	Brain Cingulate Gyrus	brain
19	chr19:19436800-19455600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:19438200-19469600	Strong transcription	Thymus	Thymus
21	chr19:19438600-19460800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:19438800-19468800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:19439600-19461000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:19439600-19469800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:19439800-19453200	Strong transcription	Right Ventricle	heart
26	chr19:19440000-19470400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:19440400-19468400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:19440400-19468600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:19440400-19469200	Strong transcription	Lung	lung
32	chr19:19440400-19469400	Strong transcription	Liver	Liver
33	chr19:19440400-19475400	Weak transcription	Right Atrium	heart
34	chr19:19440600-19468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:19440600-19468800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:19440800-19468600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr19:19440800-19470400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr19:19440800-19470600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr19:19441200-19468600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr19:19441600-19470400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:19441800-19460800	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:19444600-19460800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:19445200-19468000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:19446000-19468000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:19446200-19452800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:19446600-19452800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr19:19446600-19452800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:19446600-19470800	Strong transcription	Fetal Intestine Small	intestine
49	chr19:19446800-19452200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:19446800-19467400	Strong transcription	Fetal Muscle Trunk	muscle

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