Variant report

Variant	rs9728343
Chromosome Location	chr1:246057046-246057047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10924363	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs10924368	0.82[CHB][hapmap]
rs10924369	0.81[CHD][hapmap];0.80[GIH][hapmap]
rs10924370	0.86[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs10924371	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs10924374	0.82[ASN][1000 genomes]
rs10924375	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs11576912	0.83[CHB][hapmap]
rs11578670	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs11578736	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11582855	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11586340	0.87[AMR][1000 genomes]
rs12028528	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12028766	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12030943	0.83[CHB][hapmap]
rs12031034	0.83[CHB][hapmap]
rs12031507	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs12036477	0.83[CHB][hapmap]
rs12038045	0.83[CHB][hapmap]
rs12038841	0.82[ASN][1000 genomes]
rs12040825	0.82[ASN][1000 genomes]
rs12119771	0.87[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs12120581	0.82[CHB][hapmap]
rs12123048	0.89[CHB][hapmap]
rs12123605	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12124226	0.86[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap]
rs12127706	0.88[CHB][hapmap]
rs12744526	0.83[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1317875	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs1890814	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs1890817	0.95[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs2153403	0.87[ASW][hapmap];0.86[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs2185370	0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs2185373	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2362258	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2362262	0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2362583	0.83[CHB][hapmap]
rs2362587	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs2362590	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs34210654	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34501534	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35540445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35961285	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654062	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4654146	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs4654148	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4654149	0.83[ASN][1000 genomes]
rs4654163	0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4654164	1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9287182	0.81[CHB][hapmap]
rs9287183	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs9287185	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs9287186	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]
rs9287187	0.95[CHB][hapmap]
rs9287188	0.87[CHB][hapmap]
rs9287193	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs9287195	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9701262	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9725231	0.83[CHB][hapmap]
rs9725264	0.86[CHB][hapmap]
rs9725967	0.83[CHB][hapmap]
rs9728929	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9729305	0.95[CHB][hapmap]
rs9730400	0.95[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv998801	chr1:245924108-246131115	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv535386	chr1:245924108-246131115	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1014841	chr1:245936464-246143222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv535387	chr1:245936464-246143222	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1008786	chr1:245948622-246514454	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv535388	chr1:245948622-246514454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv468805	chr1:245950642-246229245	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv549521	chr1:245950642-246229245	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
19	nsv873405	chr1:245959911-246093644	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
23	nsv1005074	chr1:245999762-246141613	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1013699	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv535393	chr1:246005308-246143361	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv1003768	chr1:246024121-246169054	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	esv2756893	chr1:246028579-246116002	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	esv2759011	chr1:246028579-246116002	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv1014150	chr1:246038971-246208095	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
30	esv3346045	chr1:246048030-246057611	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv1003627	chr1:246051016-246352723	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv535394	chr1:246051016-246352723	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	esv3441788	chr1:246057018-246057351	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246019200-246067400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr1:246036800-246057800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:246038800-246068200	Weak transcription	Gastric	stomach
4	chr1:246039200-246080000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:246040600-246057800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:246045200-246095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:246045800-246058200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:246047800-246057600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:246051200-246057800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:246055000-246057600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:246055400-246077600	Weak transcription	Primary B cells from cord blood	blood
12	chr1:246055800-246057600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:246056600-246089200	Weak transcription	Ovary	ovary
14	chr1:246056800-246058400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr1:246056800-246059200	ZNF genes & repeats	K562	blood
16	chr1:246057000-246057200	Strong transcription	Osteobl	bone
17	chr1:246057000-246059200	Weak transcription	Thymus	Thymus
18	chr1:246057000-246059600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links