Variant report

Variant	rs2965195
Chromosome Location	chr19:19463032-19463033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19462764-19463040	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19453934..19460273-chr19:19460288..19468289,13	K562	blood:
2	chr19:19458586..19461455-chr19:19461593..19463807,2	MCF-7	breast:
3	chr19:19461132..19464795-chr19:19465298..19468375,4	K562	blood:
4	chr19:19447352..19449324-chr19:19462944..19465029,2	MCF-7	breast:
5	chr19:19456159..19458001-chr19:19462713..19465348,2	MCF-7	breast:
6	chr19:19462284..19464555-chr19:19465429..19467545,2	MCF-7	breast:
7	chr19:19461877..19465035-chr19:19465526..19468504,4	K562	blood:

No data

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

Extended variants
information (count: 81 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10406278	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10407933	0.81[CEU][hapmap]
rs10423874	0.87[CEU][hapmap]
rs1064395	0.81[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11085264	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11555053	0.81[CEU][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11668203	0.83[EUR][1000 genomes]
rs11669730	0.88[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap]
rs11670775	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs1529745	0.82[EUR][1000 genomes]
rs1557723	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1560687	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs17216041	0.81[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs17684164	1.00[CEU][hapmap]
rs17751061	0.87[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1989867	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2010506	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2011503	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2074302	0.83[AMR][1000 genomes]
rs2315023	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2315282	0.84[EUR][1000 genomes]
rs2860494	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2905429	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2905433	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2905434	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2916072	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2916075	0.83[EUR][1000 genomes]
rs2965178	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965179	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965181	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965184	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965190	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	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34487417	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4239639	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808206	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4808934	0.81[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs4808944	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4808968	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs55762233	0.81[AMR][1000 genomes]
rs55765017	0.81[AMR][1000 genomes]
rs55822665	0.85[AMR][1000 genomes]
rs56044734	0.81[AMR][1000 genomes]
rs56135441	0.81[AMR][1000 genomes]
rs56144632	0.81[AMR][1000 genomes]
rs56212061	0.82[AMR][1000 genomes]
rs56278919	0.81[AMR][1000 genomes]
rs56291054	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57436187	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58074958	0.83[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6511029	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7252453	0.94[CEU][hapmap]
rs72999059	0.81[AMR][1000 genomes]
rs72999063	0.81[AMR][1000 genomes]
rs72999068	0.83[AMR][1000 genomes]
rs751857	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs754256	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs756999	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8100097	0.80[AMR][1000 genomes]
rs8101219	0.96[GIH][hapmap]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs8105642	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs8111093	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs998732	0.81[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][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
rs2965195	LOC440518	cis	parietal	SCAN
rs2965195	LSM4	cis	cerebellum	SCAN
rs2965195	DDX49	cis	cerebellum	SCAN
rs2965195	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs2965195	OCEL1	cis	parietal	SCAN
rs2965195	JUND	cis	parietal	SCAN
rs2965195	GATAD2A	cis	parietal	SCAN
rs2965195	IL12RB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19433400-19469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19433400-19470600	Strong transcription	Fetal Stomach	stomach
3	chr19:19433800-19468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:19433800-19469800	Strong transcription	Fetal Intestine Large	intestine
5	chr19:19433800-19470400	Strong transcription	Placenta	Placenta
6	chr19:19434200-19469000	Strong transcription	Fetal Thymus	thymus
7	chr19:19434200-19469800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:19434200-19469800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:19434600-19466000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19434800-19470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:19435000-19471000	Strong transcription	Fetal Brain Female	brain
12	chr19:19435600-19468600	Strong transcription	Dnd41	blood
13	chr19:19435600-19470400	Strong transcription	Brain Germinal Matrix	brain
14	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
15	chr19:19438200-19469600	Strong transcription	Thymus	Thymus
16	chr19:19438800-19468800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:19439600-19469800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr19:19440000-19470400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:19440400-19468400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr19:19440400-19468600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19440400-19469200	Strong transcription	Lung	lung
24	chr19:19440400-19469400	Strong transcription	Liver	Liver
25	chr19:19440400-19475400	Weak transcription	Right Atrium	heart
26	chr19:19440600-19468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:19440600-19468800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr19:19440800-19468600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr19:19440800-19470400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr19:19440800-19470600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:19441200-19468600	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr19:19441600-19470400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr19:19445200-19468000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:19446000-19468000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19446600-19470800	Strong transcription	Fetal Intestine Small	intestine
36	chr19:19446800-19467400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:19447200-19467400	Strong transcription	Fetal Muscle Leg	muscle
38	chr19:19448000-19468600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:19449000-19469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:19449200-19470000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:19449400-19469000	Strong transcription	Adipose Nuclei	Adipose
42	chr19:19449800-19468600	Weak transcription	Fetal Brain Male	brain
43	chr19:19450000-19469200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:19451400-19468800	Strong transcription	Primary T cells from cord blood	blood
45	chr19:19451400-19468800	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr19:19451400-19469800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:19451600-19468200	Strong transcription	Ovary	ovary
48	chr19:19451600-19468400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr19:19451600-19468400	Strong transcription	Left Ventricle	heart
50	chr19:19451600-19468400	Strong transcription	Rectal Smooth Muscle	rectum

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