Variant report

Variant	rs10939561
Chromosome Location	chr4:9851542-9851543
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10012880	0.87[EUR][1000 genomes]
rs10939558	0.82[EUR][1000 genomes]
rs10939600	0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10939602	0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726221	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11737821	0.83[EUR][1000 genomes]
rs13105954	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13119059	0.83[EUR][1000 genomes]
rs13141635	0.82[EUR][1000 genomes]
rs13142238	0.82[EUR][1000 genomes]
rs13148571	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13152172	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1320054	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1519098	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1914874	0.87[EUR][1000 genomes]
rs1980219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292917	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28591077	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35512765	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35629527	0.84[EUR][1000 genomes]
rs4613568	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4697691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4697900	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4697902	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4697908	0.88[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6449046	0.86[EUR][1000 genomes]
rs6449089	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6449090	0.89[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6810736	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6812007	0.89[CHB][hapmap];0.84[JPT][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]
rs6828040	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6831580	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6831796	0.89[JPT][hapmap]
rs6836878	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6838891	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848689	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6852425	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];0.99[ASN][1000 genomes]
rs6858614	0.85[AMR][1000 genomes]
rs7669444	0.84[CHB][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7683831	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7688167	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7696971	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9684729	0.89[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993652	0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[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	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
5	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv878671	chr4:9766888-9912101	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878672	chr4:9786732-10008305	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv878674	chr4:9797703-9900314	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv878675	chr4:9797703-9915741	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv878676	chr4:9797703-9978094	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv878677	chr4:9797703-10008305	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1007593	chr4:9802146-9956285	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv878679	chr4:9802853-9859897	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv878680	chr4:9802853-9907336	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
16	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
17	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
18	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
19	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS 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 miRNA	56 gene(s)	inside rSNPs	diseases
20	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
21	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
22	nsv1001175	chr4:9805668-9897520	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1001832	chr4:9811805-9897520	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
25	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
26	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
27	nsv1004311	chr4:9825814-9978414	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv878682	chr4:9826870-9857956	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv461259	chr4:9834107-9863698	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv593690	chr4:9834107-9863698	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv998425	chr4:9834666-9961280	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv878683	chr4:9844621-9911843	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9845000-9851600	Weak transcription	Fetal Intestine Small	intestine
2	chr4:9845000-9874800	Weak transcription	NHEK	skin
3	chr4:9848600-9853200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:9848600-9861800	Weak transcription	HMEC	breast
5	chr4:9849200-9852400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:9850200-9851600	Enhancers	Fetal Kidney	kidney
7	chr4:9850200-9858800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:9850600-9852200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:9850600-9853000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:9851000-9851600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:9851200-9869800	Weak transcription	Gastric	stomach
12	chr4:9851400-9859000	Weak transcription	HepG2	liver

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