Variant report

Variant	rs2965184
Chromosome Location	chr19:19545428-19545429
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	chr19:19545407-19545443	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD1	chr19:19545041-19546089	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:19545400-19545456	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:19545350-19546177	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19514840..19518062-chr19:19543803..19546421,4	K562	blood:

Variant related genes	Relation type
MIR640	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10406278	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10407933	0.81[CEU][hapmap]
rs10423874	0.87[CEU][hapmap]
rs1064395	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs11085264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11555053	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs11668203	0.99[EUR][1000 genomes]
rs11669558	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11669730	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670687	0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11670761	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs11671253	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1529745	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1560687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17216041	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17751061	0.87[CEU][hapmap];1.00[TSI][hapmap]
rs2010506	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs2011503	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2860494	0.83[EUR][1000 genomes]
rs2905429	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2905433	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2905434	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2916072	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2916075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965178	0.84[EUR][1000 genomes]
rs2965179	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965181	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2965187	0.87[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2965201	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34487417	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34667451	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs45556231	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs45631651	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808204	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808205	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808206	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808934	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808958	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808969	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808970	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55927782	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56280531	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56291054	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56330647	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58074958	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61744761	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs6511029	0.82[EUR][1000 genomes]
rs7245689	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs7256028	0.89[EUR][1000 genomes]
rs751857	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs754256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs8100927	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8111093	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs998732	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2965184	IL12RB1	cis	parietal	SCAN
rs2965184	GATAD2A	cis	parietal	SCAN
rs2965184	LSM4	cis	cerebellum	SCAN
rs2965184	OCEL1	cis	parietal	SCAN
rs2965184	EDG4	cis	multi-tissue	Pritchard
rs2965184	DDX49	cis	cerebellum	SCAN
rs2965184	JUND	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19518600-19549800	Weak transcription	Fetal Brain Female	brain
2	chr19:19520800-19546800	Weak transcription	Hela-S3	cervix
3	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:19530200-19547400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:19534800-19548400	Weak transcription	HSMM	muscle
7	chr19:19537000-19546800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:19537000-19549000	Weak transcription	Brain Germinal Matrix	brain
9	chr19:19537200-19549200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:19537800-19549800	Weak transcription	A549	lung
11	chr19:19538000-19546800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:19538200-19546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:19538200-19554800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:19538400-19555000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:19538400-19555200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:19538400-19555800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:19538400-19556800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:19538400-19556800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:19539400-19547000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:19539600-19545600	Weak transcription	Primary B cells from cord blood	blood
21	chr19:19539600-19545600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:19539800-19545600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:19539800-19555000	Weak transcription	Stomach Mucosa	stomach
24	chr19:19540000-19546800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr19:19540200-19548400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:19540200-19555400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:19540200-19562600	Weak transcription	Fetal Intestine Large	intestine
28	chr19:19540400-19545600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:19540800-19549000	Weak transcription	Esophagus	oesophagus
30	chr19:19541000-19545600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:19541000-19545600	Weak transcription	Gastric	stomach
32	chr19:19541400-19548600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:19541600-19545600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:19541600-19545600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:19541600-19546800	Weak transcription	Fetal Stomach	stomach
36	chr19:19542600-19546200	Enhancers	Right Ventricle	heart
37	chr19:19542600-19547800	Enhancers	Left Ventricle	heart
38	chr19:19542800-19546000	Enhancers	Fetal Muscle Leg	muscle
39	chr19:19543000-19545600	Enhancers	HepG2	liver
40	chr19:19543200-19546000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr19:19543400-19546200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:19543400-19547200	Strong transcription	Primary T cells from cord blood	blood
43	chr19:19543400-19549000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:19543400-19550800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:19543600-19545800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr19:19543600-19545800	Enhancers	Psoas Muscle	Psoas
47	chr19:19543600-19546000	Enhancers	Pancreas	Pancrea
48	chr19:19543600-19546200	Enhancers	Ovary	ovary
49	chr19:19543600-19546400	Enhancers	Right Atrium	heart
50	chr19:19543600-19548400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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