Variant report

Variant	rs2060275
Chromosome Location	chr19:19536208-19536209
allele	C/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	ZNF263	chr19:19536083-19536398	HEK293-T-REx	kidney:	n/a	n/a
2	RUNX3	chr19:19536043-19536356	GM12878	blood:	n/a	chr19:19536215-19536230
3	RUNX3	chr19:19536079-19536370	GM12878	blood:	n/a	chr19:19536215-19536230

No.	Distal block	Cell Line	Cell type
1	chr19:19534345..19537277-chr19:19547250..19548904,2	K562	blood:
2	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:
3	chr19:19535471..19538013-chr19:19538156..19542143,4	K562	blood:

Variant related genes	Relation type
GATAD2A	TF binding region
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10406278	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10407933	0.82[CEU][hapmap]
rs10423874	0.87[CEU][hapmap]
rs1064395	0.81[CEU][hapmap]
rs11085264	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11555053	0.81[CEU][hapmap]
rs11668203	0.99[EUR][1000 genomes]
rs11669558	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11669730	0.88[CEU][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[CEU][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11671253	0.81[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[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17216041	0.81[CEU][hapmap]
rs17684164	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17751061	0.88[CEU][hapmap]
rs2010506	0.89[YRI][hapmap]
rs2011503	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2860494	0.81[EUR][1000 genomes]
rs2905429	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2905433	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2905434	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2916072	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2916075	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2965178	0.82[EUR][1000 genomes]
rs2965179	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965181	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2965187	0.88[AFR][1000 genomes]
rs2965190	0.83[CEU][hapmap]
rs2965195	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2965201	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34487417	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34667451	0.81[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	0.87[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	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808934	0.81[CEU][hapmap]
rs4808951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808958	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808968	1.00[CEU][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	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56291054	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56330647	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58074958	0.96[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]
rs7245689	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];0.90[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	0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs754256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs8100927	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8101219	0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8111093	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs998732	0.81[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2060275	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr19:19521000-19545400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19521800-19537600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19522000-19545000	Weak transcription	Fetal Lung	lung
6	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:19522600-19537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:19525400-19538200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr19:19528800-19539000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:19528800-19544200	Weak transcription	Fetal Heart	heart
12	chr19:19529000-19537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:19529000-19539000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:19529200-19537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:19530000-19539000	Weak transcription	Placenta	Placenta
16	chr19:19530000-19539000	Weak transcription	NHLF	lung
17	chr19:19530000-19545400	Weak transcription	Colonic Mucosa	Colon
18	chr19:19530200-19537000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:19530200-19537800	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:19530200-19543400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:19530200-19547400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:19530400-19536800	Strong transcription	Fetal Intestine Small	intestine
23	chr19:19531200-19538000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:19531400-19541600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:19531400-19545000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr19:19531600-19537400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr19:19531800-19538000	Enhancers	Liver	Liver
28	chr19:19532000-19536600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:19532000-19538000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:19532200-19538000	Weak transcription	Dnd41	blood
31	chr19:19532200-19539400	Weak transcription	Stomach Mucosa	stomach
32	chr19:19532200-19541400	Weak transcription	Small Intestine	intestine
33	chr19:19532400-19536600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:19532400-19536800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19532400-19537600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:19532400-19537600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr19:19532400-19537600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr19:19532400-19537600	Weak transcription	NHEK	skin
39	chr19:19532400-19539000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr19:19532400-19539200	Weak transcription	NHDF-Ad	bronchial
41	chr19:19532400-19540000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:19532400-19543400	Weak transcription	Primary T cells from cord blood	blood
43	chr19:19532400-19544400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr19:19532400-19545000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:19532600-19536400	Weak transcription	Fetal Thymus	thymus
46	chr19:19532600-19537600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:19532600-19537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr19:19532600-19538200	Weak transcription	Primary B cells from cord blood	blood
49	chr19:19532600-19539000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:19533200-19539200	Weak transcription	Gastric	stomach

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