Variant report

Variant	rs2916070
Chromosome Location	chr19:19524105-19524106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19523518..19525065-chr19:19573310..19574846,2	MCF-7	breast:
2	chr19:19523469..19525649-chr19:19548128..19551006,2	K562	blood:
3	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10406278	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[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];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11555053	0.81[CEU][hapmap];1.00[TSI][hapmap]
rs11668203	0.96[EUR][1000 genomes]
rs11669558	0.84[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];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670687	0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670761	0.82[AMR][1000 genomes];0.85[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];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs11671253	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1529745	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1557723	0.85[AMR][1000 genomes];0.82[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];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17216041	0.81[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs17684164	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17751061	0.87[CEU][hapmap];1.00[TSI][hapmap]
rs1989867	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2010506	0.85[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[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];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2060274	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2315282	0.82[EUR][1000 genomes]
rs2860494	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2905429	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905433	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905434	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2916072	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2916075	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965178	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2965179	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965181	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2965184	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]
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];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965187	0.93[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[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];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34487417	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34667451	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4239639	0.85[AMR][1000 genomes]
rs45556231	0.85[EUR][1000 genomes]
rs45631651	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4808204	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808205	0.80[AMR][1000 genomes];0.85[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];0.85[EUR][1000 genomes]
rs4808934	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs4808951	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808958	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[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];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4808969	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4808970	0.84[EUR][1000 genomes]
rs55927782	0.85[EUR][1000 genomes]
rs56280531	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56291054	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56330647	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57436187	0.82[AMR][1000 genomes]
rs58074958	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61744761	0.84[EUR][1000 genomes]
rs6511027	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs6511029	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7245689	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7256028	0.86[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];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.88[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];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs756999	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8100927	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111093	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[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
rs2916070	GATAD2A	cis	parietal	SCAN
rs2916070	JUND	cis	parietal	SCAN
rs2916070	IL12RB1	cis	parietal	SCAN
rs2916070	DDX49	cis	cerebellum	SCAN
rs2916070	EDG4	cis	multi-tissue	Pritchard
rs2916070	LSM4	cis	cerebellum	SCAN
rs2916070	OCEL1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19518400-19525200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr19:19518600-19527000	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19518600-19529400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:19518600-19549800	Weak transcription	Fetal Brain Female	brain
5	chr19:19518800-19525000	Weak transcription	HUVEC	blood vessel
6	chr19:19518800-19528200	Weak transcription	Brain Germinal Matrix	brain
7	chr19:19520400-19525000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr19:19520600-19529200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:19520800-19528000	Weak transcription	Brain Substantia Nigra	brain
10	chr19:19520800-19528800	Weak transcription	Primary B cells from cord blood	blood
11	chr19:19520800-19546800	Weak transcription	Hela-S3	cervix
12	chr19:19521000-19525600	Weak transcription	A549	lung
13	chr19:19521000-19528200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:19521000-19529000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:19521000-19545400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:19521200-19527200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:19521200-19528000	Weak transcription	Thymus	Thymus
18	chr19:19521400-19528800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:19521600-19526800	Weak transcription	Osteobl	bone
20	chr19:19521600-19528000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:19521600-19528200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19521600-19529800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:19521600-19530000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:19521600-19531600	Weak transcription	Brain Anterior Caudate	brain
25	chr19:19521800-19529600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:19521800-19536200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:19521800-19537600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:19522000-19524200	Strong transcription	NHEK	skin
29	chr19:19522000-19527000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:19522000-19527000	Weak transcription	Liver	Liver
31	chr19:19522000-19527200	Weak transcription	HSMM	muscle
32	chr19:19522000-19527800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:19522000-19528200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:19522000-19528600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:19522000-19528600	Weak transcription	NHDF-Ad	bronchial
36	chr19:19522000-19531800	Weak transcription	HepG2	liver
37	chr19:19522000-19545000	Weak transcription	Fetal Lung	lung
38	chr19:19522200-19524600	Strong transcription	Fetal Intestine Small	intestine
39	chr19:19522200-19525200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19522200-19527000	Weak transcription	Pancreas	Pancrea
41	chr19:19522200-19527800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:19522200-19528200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:19522200-19528600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:19522200-19529000	Weak transcription	Colonic Mucosa	Colon
45	chr19:19522200-19529000	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr19:19522200-19529800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:19522200-19531800	Weak transcription	Fetal Intestine Large	intestine
48	chr19:19522200-19534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion

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