Variant report

Variant	rs9660393
Chromosome Location	chr1:246094206-246094207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10754487	0.91[EUR][1000 genomes]
rs10754488	0.92[ASN][1000 genomes]
rs10802299	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10802300	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10924391	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10924401	0.80[EUR][1000 genomes]
rs10924402	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11810185	0.87[ASN][1000 genomes]
rs12041507	0.84[ASN][1000 genomes]
rs12041513	0.84[ASN][1000 genomes]
rs12562286	1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12562426	0.96[EUR][1000 genomes]
rs12566398	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12736658	0.83[ASN][1000 genomes]
rs12750953	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1577988	1.00[CEU][hapmap]
rs1933525	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2095754	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275312	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2275313	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275317	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2275318	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738057	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4255351	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4390144	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4427373	0.84[ASN][1000 genomes]
rs4449989	0.84[ASN][1000 genomes]
rs4509546	0.81[ASN][1000 genomes]
rs4654071	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs4654168	0.81[CEU][hapmap]
rs4654174	0.83[ASN][1000 genomes]
rs4654175	0.83[ASN][1000 genomes]
rs4999906	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs57935195	0.80[EUR][1000 genomes]
rs58571008	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426327	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs6662489	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6666440	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6675574	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6686870	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6686951	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6689875	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7355113	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74154341	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74154342	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs954702	0.90[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9659273	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	esv3399499	chr1:246074488-246122311	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv1013841	chr1:246080712-246317730	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246045200-246095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:246067200-246101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:246069000-246097200	Weak transcription	Primary T cells from cord blood	blood
4	chr1:246069000-246111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:246078400-246094400	Weak transcription	Primary B cells from cord blood	blood
6	chr1:246083000-246103000	Weak transcription	HSMM	muscle
7	chr1:246088000-246095200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:246088400-246095000	Strong transcription	K562	blood
9	chr1:246089200-246094600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:246090800-246101400	Weak transcription	Placenta	Placenta
11	chr1:246090800-246101800	Weak transcription	Fetal Kidney	kidney
12	chr1:246091200-246094400	Weak transcription	Ovary	ovary
13	chr1:246091400-246095600	Weak transcription	Fetal Stomach	stomach
14	chr1:246091400-246095800	Weak transcription	Aorta	Aorta
15	chr1:246091400-246103200	Weak transcription	Spleen	Spleen
16	chr1:246091400-246103400	Weak transcription	Lung	lung
17	chr1:246091800-246097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:246092800-246094400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:246092800-246094400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:246092800-246116600	Weak transcription	Osteobl	bone
21	chr1:246093000-246094600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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