Variant report

Variant	rs2431241
Chromosome Location	chr5:112144023-112144024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112137172..112140072-chr5:112143234..112145432,3	K562	blood:
2	chr5:112133420..112135351-chr5:112144014..112145746,2	K562	blood:
3	chr5:112141581..112144908-chr5:112147398..112149165,3	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10051624	0.83[AMR][1000 genomes]
rs10071425	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10072068	0.89[CEU][hapmap]
rs10075281	0.91[ASW][hapmap];0.89[CEU][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs10213844	0.81[AMR][1000 genomes]
rs11241182	0.91[ASW][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap]
rs11241183	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11241184	0.84[AMR][1000 genomes]
rs11241185	0.91[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11749701	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12513787	0.81[AMR][1000 genomes]
rs12518091	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12656359	0.84[EUR][1000 genomes]
rs12658609	0.83[AMR][1000 genomes]
rs13156251	0.89[CEU][hapmap];0.88[AFR][1000 genomes]
rs13173990	0.89[CEU][hapmap]
rs1465910	0.82[CEU][hapmap]
rs149130	0.82[ASW][hapmap]
rs1530256	0.85[CEU][hapmap]
rs1816769	0.82[CEU][hapmap]
rs1866924	0.83[ASW][hapmap];0.85[CEU][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs1914	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1966476	0.81[ASN][1000 genomes]
rs1968557	0.81[CEU][hapmap]
rs1974786	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2019720	0.92[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2229992	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs2251913	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253987	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2289484	0.91[ASW][hapmap];0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2431239	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431512	0.91[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2431514	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2439589	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2439595	0.84[CHB][hapmap]
rs2464803	0.83[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545155	0.84[AMR][1000 genomes]
rs2545156	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs2545158	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2546106	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2546107	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2546108	1.00[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2546110	0.91[ASW][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs2546112	0.83[AMR][1000 genomes]
rs2546117	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2707763	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs2707765	0.93[CEU][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28373740	0.85[AMR][1000 genomes]
rs28578275	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2901844	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2909786	0.82[CEU][hapmap]
rs2909787	0.82[CEU][hapmap]
rs2909958	0.85[CEU][hapmap]
rs3317	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[TSI][hapmap]
rs351768	0.81[CEU][hapmap]
rs351772	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35414976	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs368575	0.81[CEU][hapmap]
rs373059	0.81[AMR][1000 genomes]
rs374613	0.81[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs382427	0.81[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs3846716	0.87[TSI][hapmap]
rs390092	0.87[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs395858	0.80[CEU][hapmap];0.82[AMR][1000 genomes]
rs396321	0.91[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs4099181	0.85[CEU][hapmap]
rs41116	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs414098	0.96[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs419155	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[TSI][hapmap]
rs448162	0.83[ASW][hapmap]
rs448475	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs454886	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs458906	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs460137	0.81[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs467033	0.91[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs469886	0.81[CEU][hapmap]
rs4705486	0.91[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705559	0.91[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4705573	0.89[CEU][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4705608	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705610	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705624	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs511906	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518013	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs548710	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566419	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs62364017	0.82[AMR][1000 genomes]
rs6594646	0.91[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6862050	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6864688	0.89[CEU][hapmap]
rs6879057	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6894351	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs7704618	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs818428	0.81[CEU][hapmap]
rs818797	0.81[CEU][hapmap]
rs861674	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs9326862	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs9326863	0.91[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes]
rs9647582	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9647583	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2431241	REEP5	cis	cerebellum	SCAN
rs2431241	NCRNA00219	cis	parietal	SCAN

Chromatin state (count:123 , 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	chr5:112100000-112152200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:112104600-112155400	Weak transcription	Psoas Muscle	Psoas
5	chr5:112115800-112151200	Weak transcription	NHEK	skin
6	chr5:112118200-112151200	Weak transcription	Gastric	stomach
7	chr5:112118200-112155600	Weak transcription	Right Ventricle	heart
8	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
9	chr5:112124000-112144800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:112129000-112144200	Weak transcription	Esophagus	oesophagus
11	chr5:112129000-112149800	Weak transcription	Left Ventricle	heart
12	chr5:112129000-112151600	Weak transcription	Hela-S3	cervix
13	chr5:112129000-112154600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
16	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:112129800-112154800	Weak transcription	NH-A	brain
18	chr5:112130400-112145800	Weak transcription	Placenta	Placenta
19	chr5:112130600-112150000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:112130600-112150200	Weak transcription	NHLF	lung
21	chr5:112130600-112154800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:112130600-112155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:112130600-112155600	Weak transcription	Fetal Heart	heart
24	chr5:112130800-112146600	Weak transcription	HSMMtube	muscle
25	chr5:112130800-112149800	Weak transcription	Lung	lung
26	chr5:112130800-112150000	Weak transcription	Spleen	Spleen
27	chr5:112130800-112150200	Weak transcription	Aorta	Aorta
28	chr5:112130800-112151200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:112130800-112151400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:112130800-112154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:112130800-112155400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:112131000-112144200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:112131200-112146400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:112131200-112151200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:112131200-112151200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:112131400-112146600	Weak transcription	Ovary	ovary
37	chr5:112131400-112151200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:112131800-112157800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:112132000-112150800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:112132000-112154800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:112132200-112146800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:112132200-112151200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112132200-112155200	Weak transcription	Fetal Brain Male	brain
46	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:112133400-112150400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:112133400-112151200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:112133400-112154800	Weak transcription	HepG2	liver
50	chr5:112133600-112150000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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