Variant report

Variant	rs2905421
Chromosome Location	chr19:19457908-19457909
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19457293-19458641	K562	blood:	n/a	n/a
2	POLR2A	chr19:19457567-19458790	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:19457781-19457908	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19453934..19460273-chr19:19460288..19468289,13	K562	blood:
2	chr19:19431656..19433279-chr19:19456145..19458493,2	K562	blood:
3	chr19:19429717..19431610-chr19:19457097..19460647,3	K562	blood:
4	chr19:19457654..19459677-chr19:19465329..19466854,2	K562	blood:
5	chr19:19456159..19458001-chr19:19462713..19465348,2	MCF-7	breast:
6	chr19:19430396..19433402-chr19:19454872..19458235,4	MCF-7	breast:

No data

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

Extended variants
information (count: 104 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1000237	0.88[CEU][hapmap]
rs1009136	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1010207	0.88[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10282	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs10407952	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10409234	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10414830	0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10419245	0.88[EUR][1000 genomes]
rs10419912	0.92[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10422819	0.92[CEU][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs10426780	0.87[EUR][1000 genomes]
rs1054284	0.92[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap]
rs1063966	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs12460764	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12977937	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12985655	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13964	0.96[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1469712	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1469713	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs15622	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1858999	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2017964	0.88[EUR][1000 genomes]
rs2023882	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2074089	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2074090	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2074091	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2074296	0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2074298	0.85[EUR][1000 genomes]
rs2074299	0.88[EUR][1000 genomes]
rs2074303	0.88[CEU][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs2074550	0.88[CEU][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs2269873	0.88[CEU][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2285627	0.96[CEU][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2285859	0.81[EUR][1000 genomes]
rs2288852	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs2301669	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2301784	0.87[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2301786	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2304098	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs2315022	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2315025	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2315281	0.81[EUR][1000 genomes]
rs2315610	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2905423	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905424	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2905425	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2916074	0.88[CEU][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs2916076	0.87[CEU][hapmap];0.96[YRI][hapmap]
rs2965180	0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs2965183	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs2965185	0.80[CEU][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2965188	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2965189	0.88[CEU][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs2965191	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965193	0.94[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2965198	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965199	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34277109	0.96[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs3752151	0.92[CEU][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap]
rs3764567	0.92[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs3794990	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs3794993	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs3934667	0.88[AFR][1000 genomes]
rs4808193	0.89[EUR][1000 genomes]
rs4808200	0.96[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4808203	0.92[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs4808208	0.92[CEU][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs4808931	0.83[MEX][hapmap];0.84[YRI][hapmap]
rs4808937	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808938	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808939	0.90[EUR][1000 genomes]
rs4808940	0.90[EUR][1000 genomes]
rs4808941	0.87[EUR][1000 genomes]
rs4808942	0.88[EUR][1000 genomes]
rs4808957	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs4808959	0.92[CEU][hapmap];0.92[YRI][hapmap]
rs4808961	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs4808964	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs4808965	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs4808967	0.92[CEU][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs62135552	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6511026	0.88[CEU][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6511028	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6511030	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6511032	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67720221	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6909	0.92[CEU][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap]
rs7245983	0.92[CEU][hapmap]
rs7246748	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7247309	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7254230	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7254748	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7254927	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs735273	0.87[CEU][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs747050	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs769267	0.88[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8101938	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8103197	0.96[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8103496	0.88[CEU][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs892021	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs892022	0.92[CEU][hapmap];0.92[YRI][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2905421	RFXANK	cis	cerebellum	SCAN
rs2905421	ATP13A1	cis	brain	seeQTL
rs2905421	TM6SF2	cis	cerebellum	SCAN
rs2905421	DDX49	cis	cerebellum	SCAN
rs2905421	EDG4	cis	multi-tissue	Pritchard
rs2905421	GATAD2A	cis	parietal	SCAN
rs2905421	KIAA0892	cis	multi-tissue	Pritchard
rs2905421	ATP13A1	cis	multi-tissue	Pritchard
rs2905421	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	chr19:19436000-19460600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:19438200-19469600	Strong transcription	Thymus	Thymus
17	chr19:19438600-19460800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:19438800-19468800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:19439600-19461000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:19439600-19469800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:19440000-19470400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:19440400-19468400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr19:19440400-19468600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:19440400-19469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:19440400-19469200	Strong transcription	Lung	lung
27	chr19:19440400-19469400	Strong transcription	Liver	Liver
28	chr19:19440400-19475400	Weak transcription	Right Atrium	heart
29	chr19:19440600-19468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19440600-19468800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr19:19440800-19468600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr19:19440800-19470400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr19:19440800-19470600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:19441200-19468600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:19441600-19470400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr19:19441800-19460800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:19444600-19460800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:19445200-19468000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:19446000-19468000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:19446600-19470800	Strong transcription	Fetal Intestine Small	intestine
41	chr19:19446800-19467400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:19447200-19467400	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:19448000-19468600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:19449000-19469800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:19449200-19458600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:19449200-19470000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:19449400-19458800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:19449400-19458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:19449400-19469000	Strong transcription	Adipose Nuclei	Adipose
50	chr19:19449800-19468600	Weak transcription	Fetal Brain Male	brain

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