Variant report

Variant	rs2309316
Chromosome Location	chr2:98524859-98524860
allele	A/C
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	EP300	chr2:98524687-98525245	GM12878	blood:	n/a	n/a
2	RCOR1	chr2:98524564-98525181	GM12878	blood:	n/a	n/a
3	MTA3	chr2:98524090-98525567	GM12878	blood:	n/a	n/a
4	BCLAF1	chr2:98524208-98525214	GM12878	blood:	n/a	n/a
5	NFIC	chr2:98524134-98525603	GM12878	blood:	n/a	n/a
6	NFATC1	chr2:98524412-98525147	GM12878	blood:	n/a	n/a
7	NFIC	chr2:98524517-98525293	GM12878	blood:	n/a	n/a
8	TBP	chr2:98524263-98525281	GM12878	blood:	n/a	n/a
9	BCLAF1	chr2:98524550-98525126	GM12878	blood:	n/a	n/a
10	FOXM1	chr2:98524474-98525553	GM12878	blood:	n/a	n/a
11	MAZ	chr2:98524611-98525568	GM12878	blood:	n/a	n/a
12	MEF2C	chr2:98524588-98525222	GM12878	blood:	n/a	chr2:98525103-98525120
13	CHD1	chr2:98524356-98525101	GM12878	blood:	n/a	n/a
14	WRNIP1	chr2:98524661-98524982	GM12878	blood:	n/a	n/a
15	EBF1	chr2:98524510-98525053	GM12878	blood:	n/a	n/a
16	RELA	chr2:98524480-98525771	GM19099	blood:	n/a	n/a
17	ELK1	chr2:98524825-98525071	GM12878	blood:	n/a	n/a
18	TCF12	chr2:98524729-98524920	GM12878	blood:	n/a	n/a
19	RFX5	chr2:98524814-98524920	GM12878	blood:	n/a	n/a
20	USF2	chr2:98524710-98524972	GM12878	blood:	n/a	n/a
21	CEBPB	chr2:98524645-98525694	GM12878	blood:	n/a	n/a
22	SMC3	chr2:98524509-98525117	GM12878	blood:	n/a	n/a
23	IKZF1	chr2:98524506-98525318	GM12878	blood:	n/a	n/a
24	CUX1	chr2:98524552-98525499	GM12878	blood:	n/a	n/a
25	FOXM1	chr2:98524669-98525629	GM12878	blood:	n/a	n/a
26	EBF1	chr2:98524231-98525732	GM12878	blood:	n/a	n/a
27	POU2F2	chr2:98524516-98525151	GM12878	blood:	n/a	chr2:98525092-98525107 chr2:98525089-98525100 chr2:98525089-98525100 chr2:98525090-98525105
28	IRF4	chr2:98524595-98524992	GM12878	blood:	n/a	n/a
29	EP300	chr2:98524525-98525395	GM12878	blood:	n/a	n/a
30	RELA	chr2:98524666-98525515	GM12878	blood:	n/a	n/a
31	EBF1	chr2:98524503-98525086	GM12878	blood:	n/a	n/a
32	IRF4	chr2:98524749-98525226	GM12878	blood:	n/a	chr2:98525078-98525092
33	NFATC1	chr2:98524412-98525143	GM12878	blood:	n/a	n/a
34	PAX5	chr2:98524482-98525178	GM12878	blood:	n/a	n/a
35	EP300	chr2:98524239-98525259	GM12878	blood:	n/a	chr2:98524336-98524350
36	MAX	chr2:98524248-98525094	GM12878	blood:	n/a	n/a
37	BCL3	chr2:98524560-98525179	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr2:98524498-98525521	GM12878	blood:	n/a	n/a
39	POU2F2	chr2:98524645-98525015	GM12891	blood:	n/a	n/a
40	POLR2A	chr2:98524756-98525018	GM12878	blood:	n/a	n/a
41	BCL11A	chr2:98524664-98525158	GM12878	blood:	n/a	n/a
42	ZNF143	chr2:98524545-98525160	GM12878	blood:	n/a	n/a
43	CTCF	chr2:98524720-98524870	GM12873	blood:	n/a	n/a
44	ATF2	chr2:98524483-98525610	GM12878	blood:	n/a	n/a
45	SPI1	chr2:98524680-98525448	GM12878	blood:	n/a	n/a
46	STAT1	chr2:98524249-98525042	GM12878	blood:	n/a	chr2:98524602-98524610
47	RUNX3	chr2:98524157-98525623	GM12878	blood:	n/a	n/a
48	TCF12	chr2:98524645-98525008	GM12878	blood:	n/a	n/a
49	PAX5	chr2:98524667-98524946	GM12878	blood:	n/a	n/a
50	PML	chr2:98524152-98525171	GM12878	blood:	n/a	chr2:98524827-98524835

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98519901..98521401-chr2:98524345..98526039,2	K562	blood:

Variant related genes	Relation type
TMEM131	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10176201	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194485	1.00[YRI][hapmap]
rs10200949	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10211231	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1071885	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865055	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs11123869	1.00[LWK][hapmap];1.00[MKK][hapmap]
rs11123924	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123949	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123966	0.90[ASN][1000 genomes]
rs11690482	0.90[ASN][1000 genomes]
rs11693874	0.86[ASN][1000 genomes]
rs11888323	0.90[ASN][1000 genomes]
rs11899171	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712123	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712176	0.83[ASN][1000 genomes]
rs13003978	0.90[ASN][1000 genomes]
rs13006817	0.90[ASN][1000 genomes]
rs13008503	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010946	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13022778	0.90[ASN][1000 genomes]
rs13034644	0.89[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405546	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1466020	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1466924	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503200	0.90[ASN][1000 genomes]
rs1922280	1.00[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs2091772	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2100058	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2141862	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279825	0.85[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2305142	0.81[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs2309317	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2309356	0.89[ASN][1000 genomes]
rs3088327	0.80[ASN][1000 genomes]
rs3762593	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560167	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6543109	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6543161	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543177	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543202	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707924	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710813	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6712517	0.84[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs6719556	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6723466	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723653	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6744331	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6748809	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6748927	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7561104	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562695	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7574437	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7577886	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582664	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7598116	0.90[ASN][1000 genomes]
rs7602412	0.86[ASN][1000 genomes]
rs7605180	0.90[ASN][1000 genomes]
rs930607	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308862	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956696	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973416	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2309316	ANKRD36B	cis	Nerve Tibial	GTEx
rs2309316	CNNM3	cis	cerebellum	SCAN
rs2309316	ADRA2B	cis	cerebellum	SCAN
rs2309316	FAM178B	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98503800-98528600	Weak transcription	NHDF-Ad	bronchial
2	chr2:98503800-98536400	Weak transcription	HSMMtube	muscle
3	chr2:98504000-98528000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:98504000-98533800	Weak transcription	Spleen	Spleen
5	chr2:98504000-98538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:98504000-98540600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:98504000-98540800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:98504200-98525400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:98504200-98530800	Weak transcription	Thymus	Thymus
10	chr2:98504400-98527000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:98504600-98525600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:98504600-98540800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:98504600-98552200	Weak transcription	NHLF	lung
14	chr2:98504800-98527400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:98505400-98528800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:98505400-98530200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:98507600-98535000	Weak transcription	Brain Anterior Caudate	brain
18	chr2:98509000-98536400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:98515800-98540800	Weak transcription	Aorta	Aorta
20	chr2:98516400-98534600	Weak transcription	A549	lung
21	chr2:98517600-98528000	Weak transcription	NH-A	brain
22	chr2:98519600-98541600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:98519800-98538600	Weak transcription	Gastric	stomach
24	chr2:98520200-98528400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:98520200-98546000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:98520200-98552200	Weak transcription	Brain Angular Gyrus	brain
27	chr2:98520600-98550600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:98520800-98540400	Weak transcription	Lung	lung
29	chr2:98521200-98532800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:98521400-98525000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:98521800-98525200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:98521800-98527400	Strong transcription	Primary T cells from cord blood	blood
33	chr2:98521800-98527600	Strong transcription	Fetal Intestine Large	intestine
34	chr2:98521800-98540400	Weak transcription	Colonic Mucosa	Colon
35	chr2:98522000-98525000	Strong transcription	Placenta	Placenta
36	chr2:98522200-98525200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:98522200-98526800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:98522200-98527200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:98522400-98525000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:98522400-98525000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:98522400-98525000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:98522400-98525600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:98522600-98525000	Strong transcription	HepG2	liver
44	chr2:98522600-98525600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:98522600-98526000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr2:98522800-98525200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:98522800-98525600	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:98522800-98527800	Weak transcription	Osteobl	bone
49	chr2:98523000-98525000	Strong transcription	Dnd41	blood
50	chr2:98523000-98525800	Strong transcription	Primary T cells fromperipheralblood	blood

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