Variant report

Variant	rs311565
Chromosome Location	chr2:86293829-86293830
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	GATA3	chr2:86293235-86293952	SH-SY5Y	brain:	n/a	chr2:86293391-86293408 chr2:86293554-86293564 chr2:86293555-86293564 chr2:86293555-86293562
2	GATA2	chr2:86292755-86294118	SH-SY5Y	brain:	n/a	chr2:86293391-86293408 chr2:86293554-86293564 chr2:86293555-86293564 chr2:86293555-86293562
3	EP300	chr2:86292386-86294615	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
POLR1A	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10165327	0.86[AMR][1000 genomes]
rs10176454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10179090	0.86[AMR][1000 genomes]
rs10183744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10187547	0.89[ASN][1000 genomes]
rs1019592	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs1025104	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs10427394	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs1075622	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs11127012	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11679343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11686963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11694973	0.98[ASN][1000 genomes]
rs12053229	0.98[ASN][1000 genomes]
rs12714168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1424517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1424520	0.87[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs1559515	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs1559516	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs1559517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1834163	0.98[ASN][1000 genomes]
rs1991106	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs2018547	0.88[ASN][1000 genomes]
rs2241436	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs2278084	0.81[AMR][1000 genomes]
rs2278086	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288118	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs2288119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2288120	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs2288121	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs2367201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2367202	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs3088038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs311562	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs311563	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311566	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311569	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs311573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	0.85[CEU][hapmap]
rs311587	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731820	0.98[ASN][1000 genomes]
rs3770069	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs3815840	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4618054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832021	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832022	0.98[ASN][1000 genomes]
rs4832241	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4832242	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs4832244	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs4832245	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs4832246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832249	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs4832250	0.87[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs4832251	0.98[ASN][1000 genomes]
rs4832255	0.91[MEX][hapmap]
rs4832257	0.82[MEX][hapmap]
rs59947468	0.92[ASN][1000 genomes]
rs60479377	0.92[ASN][1000 genomes]
rs60719866	0.92[ASN][1000 genomes]
rs61620607	0.99[ASN][1000 genomes]
rs6547659	0.81[AMR][1000 genomes]
rs6720327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6740228	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs6741577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6750581	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs6759862	0.98[ASN][1000 genomes]
rs725046	0.98[ASN][1000 genomes]
rs749581	0.82[MEX][hapmap]
rs7559420	1.00[ASN][1000 genomes]
rs7562837	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7598787	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs7606421	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs311565	POLR1A	cis	Artery Tibial	GTEx
rs311565	POLR1A	cis	Nerve Tibial	GTEx
rs311565	POLR1A	cis	Thyroid	GTEx
rs311565	POLR1A	cis	cerebellum	SCAN
rs311565	PTCD3	cis	parietal	SCAN
rs311565	C2orf89	cis	cerebellum	SCAN
rs311565	POLR1A	cis	Esophagus Muscularis	GTEx
rs311565	POLR1A	cis	Stomach	GTEx
rs311565	POLR1A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:86268800-86295000	Strong transcription	Dnd41	blood
7	chr2:86282600-86299200	Weak transcription	Small Intestine	intestine
8	chr2:86282800-86295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:86285800-86294600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:86285800-86299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:86286000-86302200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:86286200-86294200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:86286200-86298400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:86286200-86298600	Strong transcription	Fetal Lung	lung
17	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:86287000-86298800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:86287200-86294600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:86287600-86294000	Strong transcription	Primary T cells from cord blood	blood
22	chr2:86287600-86294000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:86288400-86294200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:86288800-86294200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:86289000-86294400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:86289800-86296000	Weak transcription	Stomach Mucosa	stomach
27	chr2:86289800-86307200	Strong transcription	HepG2	liver
28	chr2:86290000-86294000	Strong transcription	Left Ventricle	heart
29	chr2:86290200-86295600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:86290200-86299400	Strong transcription	Hela-S3	cervix
31	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:86290600-86294000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr2:86290600-86294200	Strong transcription	Placenta	Placenta
34	chr2:86290600-86297600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:86290600-86306200	Strong transcription	Fetal Intestine Large	intestine
36	chr2:86290800-86294200	Strong transcription	Colonic Mucosa	Colon
37	chr2:86290800-86298200	Strong transcription	Liver	Liver
38	chr2:86290800-86299400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:86290800-86314600	Strong transcription	HMEC	breast
41	chr2:86290800-86318600	Strong transcription	K562	blood
42	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:86291000-86298400	Strong transcription	Primary B cells from cord blood	blood
44	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
45	chr2:86291400-86299200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:86291600-86295200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:86291600-86295200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:86291600-86297600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:86291800-86294000	Strong transcription	Fetal Intestine Small	intestine

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