Variant report

Variant	rs2464803
Chromosome Location	chr5:112131787-112131788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112123801..112127041-chr5:112128309..112132302,4	K562	blood:
2	chr5:111495941..111497772-chr5:112131331..112133218,2	K562	blood:
3	chr5:112123613..112127041-chr5:112129146..112132302,3	K562	blood:
4	chr5:112126744..112130086-chr5:112131543..112134649,3	MCF-7	breast:
5	chr5:112129867..112132143-chr5:112136582..112139044,2	K562	blood:

Variant related genes	Relation type
ENSG00000224032	Chromatin interaction
ENSG00000238363	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10051624	0.83[AMR][1000 genomes]
rs10071425	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10075281	0.92[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs10213844	0.81[AMR][1000 genomes]
rs1093611	0.88[CHD][hapmap]
rs11241182	0.92[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[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	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11749701	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12513787	0.81[AMR][1000 genomes]
rs12518091	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12658609	0.83[AMR][1000 genomes]
rs13156251	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs149130	0.83[ASW][hapmap]
rs1530256	0.84[CHB][hapmap]
rs153546	0.88[CHD][hapmap]
rs153548	0.88[CHD][hapmap]
rs1866924	0.83[ASW][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap]
rs1914	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1968557	0.84[CHB][hapmap]
rs1974786	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2019720	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2229992	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs2251913	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2253987	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2289484	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2431239	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431241	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]
rs2431512	0.92[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431514	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439589	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439595	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2545155	0.84[AMR][1000 genomes]
rs2545156	0.90[CHD][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap]
rs2545158	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2546106	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2546107	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2546108	0.83[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2546110	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]
rs2546112	0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2546115	0.85[CHB][hapmap]
rs2546117	0.95[CHB][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2707763	0.89[CHB][hapmap];0.85[AMR][1000 genomes]
rs2707765	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28373740	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28578275	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2901844	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3317	0.83[ASW][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs351772	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35414976	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs373059	0.81[AMR][1000 genomes]
rs374613	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs382427	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs3846716	0.87[TSI][hapmap]
rs390092	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395858	0.88[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs396321	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs4099181	0.80[CEU][hapmap]
rs41116	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs414098	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs419155	0.83[ASW][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs448162	0.83[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs448475	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs454886	0.95[CHB][hapmap]
rs458906	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs460137	0.84[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs467033	0.92[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4705486	0.92[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4705559	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes]
rs4705573	0.90[CHB][hapmap];0.81[AMR][1000 genomes]
rs4705608	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705610	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4705624	1.00[CHB][hapmap];1.00[YRI][hapmap];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];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518013	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs548710	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566419	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs62364017	0.82[AMR][1000 genomes]
rs6594646	0.92[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6862050	0.82[CEU][hapmap];0.84[CHB][hapmap];0.82[AMR][1000 genomes]
rs6864688	0.85[CEU][hapmap]
rs6879057	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6894351	0.85[TSI][hapmap]
rs7704618	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs861674	0.84[TSI][hapmap]
rs9326862	0.85[TSI][hapmap]
rs9326863	0.92[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs9647582	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9647583	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs2464803	NCRNA00219	cis	parietal	SCAN
rs2464803	REEP5	cis	cerebellum	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	chr5:112100000-112152200	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	chr5:112115600-112134600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:112115600-112140000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:112115800-112151200	Weak transcription	NHEK	skin
8	chr5:112118200-112136600	Weak transcription	Pancreas	Pancrea
9	chr5:112118200-112151200	Weak transcription	Gastric	stomach
10	chr5:112118200-112155600	Weak transcription	Right Ventricle	heart
11	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
12	chr5:112122000-112132000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr5:112123600-112141800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:112124000-112144800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:112125000-112132000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr5:112125000-112140000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:112125600-112132200	Strong transcription	Fetal Thymus	thymus
18	chr5:112125600-112134800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:112125800-112132000	Strong transcription	Primary T cells from cord blood	blood
20	chr5:112126200-112131800	Strong transcription	Fetal Brain Female	brain
21	chr5:112126200-112132400	Strong transcription	Fetal Muscle Leg	muscle
22	chr5:112126800-112131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:112126800-112131800	Strong transcription	Brain Cingulate Gyrus	brain
24	chr5:112126800-112132000	Strong transcription	Adipose Nuclei	Adipose
25	chr5:112126800-112132000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:112126800-112132200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:112126800-112132400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:112126800-112134200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr5:112126800-112142000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:112127600-112132000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:112127800-112140000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:112128000-112134000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:112128200-112132200	Strong transcription	Brain Anterior Caudate	brain
34	chr5:112128200-112134000	Strong transcription	NHDF-Ad	bronchial
35	chr5:112128400-112131800	Strong transcription	Liver	Liver
36	chr5:112128400-112131800	Strong transcription	Fetal Intestine Large	intestine
37	chr5:112128400-112132200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:112128400-112133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:112128600-112131800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:112128600-112131800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:112128600-112131800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:112128600-112132000	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:112128600-112133800	Strong transcription	Brain Germinal Matrix	brain
44	chr5:112128800-112133800	Strong transcription	Brain Hippocampus Middle	brain
45	chr5:112129000-112144200	Weak transcription	Esophagus	oesophagus
46	chr5:112129000-112149800	Weak transcription	Left Ventricle	heart
47	chr5:112129000-112151600	Weak transcription	Hela-S3	cervix
48	chr5:112129000-112154600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr5:112129200-112133200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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