Variant report

Variant	rs2909904
Chromosome Location	chr5:112207007-112207008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112206451..112208757-chr5:112210968..112212741,2	MCF-7	breast:
2	chr5:112202124..112203911-chr5:112204966..112207266,2	K562	blood:
3	chr5:112196333..112202800-chr5:112202907..112207825,7	MCF-7	breast:
4	chr5:112200659..112202447-chr5:112205231..112207652,2	K562	blood:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1069061	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1093611	0.87[EUR][1000 genomes]
rs1093677	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12656359	0.81[ASN][1000 genomes]
rs151976	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151977	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151978	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153545	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs153546	0.86[EUR][1000 genomes]
rs153548	0.81[EUR][1000 genomes]
rs153550	0.83[EUR][1000 genomes]
rs153562	0.81[AMR][1000 genomes]
rs173466	0.80[AMR][1000 genomes]
rs193527	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966477	0.83[ASN][1000 genomes]
rs2545162	0.80[ASN][1000 genomes]
rs2545164	0.80[ASN][1000 genomes]
rs2545165	0.80[ASN][1000 genomes]
rs2545166	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545167	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2909786	0.81[ASN][1000 genomes]
rs2909787	0.81[ASN][1000 genomes]
rs2909958	0.82[ASN][1000 genomes]
rs2952615	0.81[ASN][1000 genomes]
rs351767	0.94[EUR][1000 genomes]
rs351769	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351770	0.86[EUR][1000 genomes]
rs351771	0.81[ASN][1000 genomes]
rs35726351	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372492	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380144	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs382260	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386830	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs397768	0.90[ASN][1000 genomes]
rs41115	0.81[ASN][1000 genomes]
rs411356	0.83[ASN][1000 genomes]
rs419632	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42427	0.81[ASN][1000 genomes]
rs429427	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs430665	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431287	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs433429	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs434090	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs434157	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs438252	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs439456	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442507	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs446567	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455412	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455469	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456313	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs458451	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459102	0.88[EUR][1000 genomes]
rs460301	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs460832	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461424	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs461866	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs463229	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs464708	0.80[ASN][1000 genomes]
rs465454	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465899	0.89[ASN][1000 genomes]
rs466443	0.88[ASN][1000 genomes]
rs468101	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs468610	0.81[EUR][1000 genomes]
rs468783	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs468854	0.82[EUR][1000 genomes]
rs469663	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469727	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs469760	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469827	0.82[EUR][1000 genomes]
rs481789	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs495794	0.94[EUR][1000 genomes]
rs497844	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs514763	0.94[EUR][1000 genomes]
rs519397	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs565453	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs565603	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs569940	0.81[ASN][1000 genomes]
rs580237	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs698405	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712662	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712663	0.85[EUR][1000 genomes]
rs712664	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712665	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712666	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712668	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712671	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213	0.97[EUR][1000 genomes]
rs818423	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs818424	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs818425	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs818426	0.89[ASN][1000 genomes]
rs818427	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs818429	0.88[EUR][1000 genomes]
rs818782	0.84[ASN][1000 genomes]
rs864682	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs866006	0.81[ASN][1000 genomes]
rs9011	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv870231	chr5:112192379-112247084	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1029595	chr5:112197662-112242375	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1030103	chr5:112197662-112255712	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537863	chr5:112197662-112255712	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv4960	chr5:112200199-112218299	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2909904	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112197800-112211800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:112198400-112211200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112198400-112220600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:112198600-112207400	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr5:112198600-112208800	Strong transcription	Fetal Thymus	thymus
6	chr5:112198800-112207200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:112198800-112208800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:112199000-112207200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:112199000-112208000	Strong transcription	Primary B cells from peripheral blood	blood
10	chr5:112199000-112226000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:112199200-112207200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:112199200-112210200	Weak transcription	Psoas Muscle	Psoas
13	chr5:112199200-112213200	Weak transcription	Fetal Heart	heart
14	chr5:112199200-112213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:112199400-112207200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:112199400-112207400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:112199400-112207600	Strong transcription	HSMMtube	muscle
18	chr5:112199400-112215000	Weak transcription	Small Intestine	intestine
19	chr5:112199600-112207200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:112199600-112207200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:112199600-112214400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:112199800-112212200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:112200000-112207600	Strong transcription	Liver	Liver
24	chr5:112200000-112209000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:112200400-112207600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:112200600-112213800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:112200600-112242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:112201000-112207800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:112201000-112209400	Strong transcription	Osteobl	bone
30	chr5:112202000-112207600	Strong transcription	Thymus	Thymus
31	chr5:112202800-112217800	Weak transcription	Brain Substantia Nigra	brain
32	chr5:112203400-112213000	Weak transcription	Fetal Lung	lung
33	chr5:112203400-112218200	Weak transcription	Colonic Mucosa	Colon
34	chr5:112203600-112214400	Weak transcription	Stomach Mucosa	stomach
35	chr5:112203800-112211000	Weak transcription	HepG2	liver
36	chr5:112204000-112207400	Strong transcription	Fetal Intestine Small	intestine
37	chr5:112204000-112212000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:112204000-112213800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:112204200-112207600	Strong transcription	Fetal Stomach	stomach
40	chr5:112205000-112214600	Weak transcription	Fetal Kidney	kidney
41	chr5:112205200-112212800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:112205400-112207400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:112205400-112207600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:112205400-112213600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:112205600-112212800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:112206200-112209400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:112206200-112218400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:112206400-112207200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr5:112206400-112208800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr5:112206400-112209400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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