Variant report

Variant	rs2949573
Chromosome Location	chr15:31251366-31251367
allele	A/G
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	POLR2A	chr15:31251298-31251454	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
RNU6-466P	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153041	0.86[CHB][hapmap]
rs10163148	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs11070678	0.92[CHB][hapmap]
rs11070718	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1133642	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631543	0.81[EUR][1000 genomes]
rs11638295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12437580	0.82[ASN][1000 genomes]
rs12439664	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12441318	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12901022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs12905872	0.86[ASN][1000 genomes]
rs12906480	0.82[ASN][1000 genomes]
rs12911057	0.85[CHB][hapmap]
rs12913397	0.88[ASN][1000 genomes]
rs12914207	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914438	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1404470	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425291	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1474381	0.92[CHB][hapmap]
rs1474382	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs1524876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2042613	1.00[CHB][hapmap]
rs2113945	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2113946	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[ASN][1000 genomes]
rs2140735	0.81[ASN][1000 genomes]
rs2272218	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs2272219	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2293314	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs2293319	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2293320	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs28564430	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28693590	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2873	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2949566	0.81[EUR][1000 genomes]
rs2949567	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2949569	0.85[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2949570	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2949571	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2949572	0.81[ASN][1000 genomes]
rs2949574	0.87[GIH][hapmap];0.91[TSI][hapmap]
rs2949575	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2949576	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs2949577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2949578	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2955783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2955787	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2955790	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955791	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs2955794	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2955795	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2955796	0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs2955798	0.81[EUR][1000 genomes]
rs2959039	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2959047	0.82[ASN][1000 genomes]
rs2959049	0.92[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959050	0.82[ASN][1000 genomes]
rs2959054	0.87[GIH][hapmap];0.91[TSI][hapmap]
rs3743231	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs3743233	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794594	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs4779794	0.80[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4779796	0.92[CHB][hapmap]
rs4779797	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs58083498	0.86[ASN][1000 genomes]
rs6493387	0.86[ASN][1000 genomes]
rs6493388	0.86[ASN][1000 genomes]
rs7161812	0.92[CHB][hapmap]
rs7164530	0.82[ASN][1000 genomes]
rs7165798	1.00[CHB][hapmap]
rs7169064	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs7170710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175256	0.82[ASN][1000 genomes]
rs7175951	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs7175967	0.84[ASN][1000 genomes]
rs7176351	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs7178375	0.92[CHB][hapmap]
rs7178533	0.92[CHB][hapmap]
rs7182143	1.00[CHB][hapmap]
rs7183880	0.82[ASN][1000 genomes]
rs798088	0.86[CHB][hapmap]
rs798101	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs8040989	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041717	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs811768	0.86[CHB][hapmap]
rs964925	0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9806159	0.92[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS 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 target site	28 gene(s)	inside rSNPs	diseases
10	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
13	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
16	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31200600-31254800	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr15:31225400-31255800	Strong transcription	Fetal Intestine Large	intestine
3	chr15:31225600-31253800	Strong transcription	Dnd41	blood
4	chr15:31225800-31256000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:31226000-31255800	Strong transcription	Fetal Stomach	stomach
6	chr15:31226000-31258800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr15:31226200-31269200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:31226400-31260800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:31226600-31254400	Strong transcription	Fetal Thymus	thymus
10	chr15:31226600-31255200	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:31227000-31269600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:31227200-31255800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:31227200-31258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:31228400-31253600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:31228400-31254400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr15:31228400-31254600	Strong transcription	Thymus	Thymus
17	chr15:31228600-31253200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:31228600-31258800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr15:31229000-31254800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:31229200-31261000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:31230400-31258800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:31233400-31269200	Strong transcription	Liver	Liver
23	chr15:31236600-31255000	Strong transcription	Rectal Smooth Muscle	rectum
24	chr15:31237200-31269600	Strong transcription	Primary B cells from cord blood	blood
25	chr15:31238200-31254600	Strong transcription	Fetal Lung	lung
26	chr15:31238600-31255200	Strong transcription	Fetal Kidney	kidney
27	chr15:31240400-31255000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:31241400-31254600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:31242000-31282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr15:31242200-31251600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:31242200-31253400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:31242200-31254600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:31242400-31255800	Strong transcription	Fetal Intestine Small	intestine
34	chr15:31242600-31253200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:31242600-31253800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:31243000-31254400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr15:31243200-31254800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:31243200-31267600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:31243400-31253000	Weak transcription	Fetal Brain Male	brain
40	chr15:31244000-31252800	Strong transcription	Colon Smooth Muscle	Colon
41	chr15:31244000-31253600	Strong transcription	HepG2	liver
42	chr15:31245000-31276400	Weak transcription	Brain Germinal Matrix	brain
43	chr15:31246400-31253200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:31246600-31252400	Strong transcription	Fetal Muscle Leg	muscle
45	chr15:31246600-31254400	Weak transcription	Right Atrium	heart
46	chr15:31246800-31254400	Weak transcription	Fetal Heart	heart
47	chr15:31247000-31254200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:31247000-31270200	Weak transcription	K562	blood
49	chr15:31247200-31253400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:31247200-31253400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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