Variant report

Variant	rs2546110
Chromosome Location	chr5:112162413-112162414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112154161..112155749-chr5:112161168..112163115,2	K562	blood:
2	chr5:112156563..112159936-chr5:112161937..112165418,3	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10072068	0.81[JPT][hapmap]
rs10075281	1.00[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs1093611	0.90[CHD][hapmap]
rs11241182	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs11241185	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs12518091	0.85[CHB][hapmap]
rs1441375	0.84[CEU][hapmap]
rs149130	0.91[ASW][hapmap]
rs1530256	0.84[CHB][hapmap]
rs153546	0.90[CHD][hapmap]
rs153548	0.90[CHD][hapmap]
rs1661035	0.88[CEU][hapmap]
rs1866924	0.92[ASW][hapmap]
rs187075	0.86[EUR][1000 genomes]
rs1914	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1966476	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1966477	0.85[EUR][1000 genomes]
rs1968557	0.84[CHB][hapmap]
rs1974786	0.94[CHB][hapmap]
rs2019720	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2229992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251913	0.89[ASN][1000 genomes]
rs2253987	0.91[ASN][1000 genomes]
rs2289484	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2431238	0.82[TSI][hapmap]
rs2431241	0.91[ASW][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs2431512	1.00[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2431514	0.87[ASN][1000 genomes]
rs2439589	0.82[ASN][1000 genomes]
rs2439591	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs2439595	1.00[CHB][hapmap]
rs2464803	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs2464805	0.85[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2545156	0.84[ASW][hapmap];0.93[CHD][hapmap]
rs2545158	0.88[ASN][1000 genomes]
rs2545159	0.83[EUR][1000 genomes]
rs2545162	0.88[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs2545163	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2545166	0.84[CEU][hapmap]
rs2545167	0.81[CEU][hapmap]
rs2545169	0.88[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2546106	0.83[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2546107	0.95[ASN][1000 genomes]
rs2546108	0.91[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs2546111	0.84[EUR][1000 genomes]
rs2546112	0.95[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2546115	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2546117	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2707763	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2707765	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs3317	0.92[ASW][hapmap];0.93[CHD][hapmap]
rs351772	0.94[ASN][1000 genomes]
rs374613	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs382427	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs386830	0.83[EUR][1000 genomes]
rs390092	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs392907	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs395266	0.83[EUR][1000 genomes]
rs395858	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs396321	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs397768	0.83[EUR][1000 genomes]
rs41116	0.84[ASN][1000 genomes]
rs411356	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs414098	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs419155	0.92[ASW][hapmap];0.93[CHD][hapmap]
rs429427	0.81[CEU][hapmap]
rs433429	0.83[EUR][1000 genomes]
rs448162	0.92[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs448475	0.84[ASN][1000 genomes]
rs454886	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs458906	0.81[ASN][1000 genomes]
rs458967	0.84[EUR][1000 genomes]
rs460137	0.84[ASW][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs464002	0.88[CEU][hapmap]
rs464708	0.88[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs467033	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4705486	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap]
rs4705559	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4705573	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4705608	0.95[CHB][hapmap]
rs4705610	1.00[ASW][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4705624	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs511906	0.89[ASN][1000 genomes]
rs518013	0.89[ASN][1000 genomes]
rs529076	0.84[EUR][1000 genomes]
rs548710	0.92[ASN][1000 genomes]
rs563556	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs566419	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6594646	1.00[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6862050	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7704618	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9326863	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2546110	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs2546110	REEP5	cis	lymphoblastoid	seeQTL
rs2546110	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
5	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:112134000-112162800	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:112149000-112163600	Weak transcription	A549	lung
15	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:112149800-112166400	Strong transcription	Fetal Thymus	thymus
17	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:112150400-112166600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:112152000-112164200	Weak transcription	HMEC	breast
21	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
22	chr5:112152000-112183800	Weak transcription	Gastric	stomach
23	chr5:112152200-112163600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:112152200-112172000	Weak transcription	NHLF	lung
25	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:112153400-112165800	Strong transcription	Liver	Liver
29	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
30	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
32	chr5:112154800-112165600	Strong transcription	Osteobl	bone
33	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
34	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:112155800-112162800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:112155800-112163200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:112155800-112163600	Weak transcription	Psoas Muscle	Psoas
38	chr5:112155800-112163800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
40	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
41	chr5:112156000-112162800	Weak transcription	HepG2	liver
42	chr5:112156000-112162800	Weak transcription	NH-A	brain
43	chr5:112156000-112163800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:112156000-112163800	Weak transcription	NHEK	skin
45	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
48	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr5:112156400-112163800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:112156800-112163000	Weak transcription	Fetal Lung	lung

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