Variant report

Variant	rs396321
Chromosome Location	chr5:112113735-112113736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:112113261-112113808	SK-N-SH	brain:	n/a	n/a
2	REST	chr5:112113209-112114047	H1-neurons	neurons:	n/a	n/a
3	GATA3	chr5:112113577-112113743	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr5:112113375-112113780	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
RNU6-482P	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10071425	0.83[EUR][1000 genomes]
rs10072068	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs10073398	0.85[EUR][1000 genomes]
rs10075281	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap]
rs10076641	0.80[EUR][1000 genomes]
rs1093611	0.90[CHD][hapmap]
rs11241182	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs11241183	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11241184	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241185	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11749701	0.80[EUR][1000 genomes]
rs11954856	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs12513804	0.92[CEU][hapmap]
rs12518091	0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12659119	0.88[EUR][1000 genomes]
rs12719151	0.80[CEU][hapmap]
rs13156251	0.80[CEU][hapmap]
rs13173990	0.80[CEU][hapmap]
rs1465910	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs149130	0.91[ASW][hapmap]
rs1530256	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs153546	0.90[CHD][hapmap]
rs153548	0.90[CHD][hapmap]
rs1816769	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1866924	0.92[ASW][hapmap]
rs1914	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1968557	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs1974786	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs2019720	0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs2020383	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2229992	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs2251913	0.81[AMR][1000 genomes]
rs2253987	0.83[AMR][1000 genomes]
rs2289484	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2431239	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2431241	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]
rs2431242	0.87[EUR][1000 genomes]
rs2431512	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431514	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439589	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2439595	1.00[CHB][hapmap]
rs2464803	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]
rs2545156	0.84[ASW][hapmap];0.93[CHD][hapmap]
rs2545158	0.82[AMR][1000 genomes]
rs2546106	0.83[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs2546108	0.91[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs2546110	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2546112	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2546115	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2546117	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2707763	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2707765	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28578275	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2901844	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2909786	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2909787	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2909958	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs3317	0.92[ASW][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap]
rs35130225	0.87[EUR][1000 genomes]
rs351772	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs35414976	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs374613	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs382427	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3846716	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs390092	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs395858	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4099181	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs414098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs419155	0.92[ASW][hapmap];0.93[CHD][hapmap]
rs448162	0.92[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs454886	0.95[CHB][hapmap]
rs458906	0.85[EUR][1000 genomes]
rs460137	0.84[ASW][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs467033	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4705486	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4705559	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap]
rs4705573	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4705608	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs4705609	0.82[EUR][1000 genomes]
rs4705610	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4705624	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4705815	0.80[CEU][hapmap]
rs511906	0.81[AMR][1000 genomes]
rs544243	0.81[CEU][hapmap]
rs548710	0.83[AMR][1000 genomes]
rs566419	0.86[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs569940	0.81[EUR][1000 genomes]
rs62364017	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6594643	0.81[CEU][hapmap]
rs6594646	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs6862050	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6864688	0.84[CEU][hapmap]
rs6867243	0.86[EUR][1000 genomes]
rs6879057	0.84[EUR][1000 genomes]
rs6894351	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6898133	0.83[CEU][hapmap]
rs7704618	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs861674	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs9326862	0.92[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9326863	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs9647582	0.85[EUR][1000 genomes]
rs9647583	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs396321	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112074400-112119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112074400-112125600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:112074400-112128600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:112079600-112128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:112079800-112128600	Weak transcription	Small Intestine	intestine
6	chr5:112081200-112128600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:112087600-112117600	Weak transcription	Gastric	stomach
8	chr5:112089800-112116600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:112093400-112114800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:112093400-112114800	Weak transcription	NHEK	skin
11	chr5:112093400-112116000	Weak transcription	HUVEC	blood vessel
12	chr5:112093400-112117400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:112093400-112128600	Weak transcription	Ovary	ovary
14	chr5:112093400-112128600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:112094200-112128600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:112094200-112128800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:112095200-112122400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:112095600-112116800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:112096200-112116000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:112096200-112117600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:112096400-112115400	Weak transcription	K562	blood
23	chr5:112097000-112116600	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:112097800-112127000	Weak transcription	Esophagus	oesophagus
25	chr5:112098000-112128600	Weak transcription	HepG2	liver
26	chr5:112098200-112114600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:112098200-112114600	Weak transcription	HMEC	breast
28	chr5:112098200-112128600	Weak transcription	Aorta	Aorta
29	chr5:112098200-112129800	Weak transcription	Spleen	Spleen
30	chr5:112098400-112130000	Weak transcription	Fetal Heart	heart
31	chr5:112098600-112116400	Weak transcription	Placenta	Placenta
32	chr5:112098600-112131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:112098800-112122400	Weak transcription	A549	lung
34	chr5:112099200-112114000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr5:112099600-112122200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112100000-112152200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:112101200-112117400	Weak transcription	Pancreas	Pancrea
38	chr5:112101600-112114000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:112101600-112118000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:112102200-112114800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:112102200-112120400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112102400-112115400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:112102400-112118400	Strong transcription	Dnd41	blood
44	chr5:112102400-112121000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:112102600-112118400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:112102800-112119000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:112104400-112125600	Weak transcription	Fetal Intestine Small	intestine
49	chr5:112104600-112115400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:112104600-112116400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links