Variant report

Variant	rs28125
Chromosome Location	chr5:115613762-115613763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115607181..115609929-chr5:115613382..115615949,2	K562	blood:
2	chr5:115611187..115613784-chr5:115614610..115617269,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10042163	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10055039	0.82[YRI][hapmap]
rs1090076	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11957456	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs12653124	0.91[CEU][hapmap]
rs1508874	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1508884	0.82[YRI][hapmap]
rs153591	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs153614	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs168833	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs194182	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2136206	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap]
rs2136212	1.00[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap]
rs253953	0.82[ASN][1000 genomes]
rs253956	0.83[ASN][1000 genomes]
rs253960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs253967	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs254149	0.84[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs254154	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27499	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36194147	0.84[ASN][1000 genomes]
rs37182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs37183	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs4463206	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[YRI][hapmap]
rs4920906	0.82[YRI][hapmap]
rs6594955	0.83[YRI][hapmap]
rs6860795	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs6878279	0.83[YRI][hapmap]
rs6896229	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs712580	0.84[ASN][1000 genomes]
rs712581	0.81[ASN][1000 genomes]
rs7701512	0.91[CEU][hapmap];0.83[YRI][hapmap]
rs7733992	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs784482	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];0.99[ASN][1000 genomes]
rs785368	0.91[CEU][hapmap]
rs804141	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes]
rs9285884	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs9326985	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs9326992	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs9687859	1.00[CEU][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882743	chr5:115501792-115634127	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1024670	chr5:115540586-115615459	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv521050	chr5:115541563-115617297	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv882745	chr5:115561128-115616288	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv34428	chr5:115575513-115626966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2753795	chr5:115576026-115626966	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2755740	chr5:115576139-115633474	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv2757134	chr5:115578810-115633474	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2759372	chr5:115578810-115633474	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2760969	chr5:115583627-115630890	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1018714	chr5:115586834-115625245	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv3692873	chr5:115594144-115617297	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv2422101	chr5:115594144-115625228	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv517704	chr5:115596120-115617297	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv818377	chr5:115596120-115617297	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv2753045	chr5:115596277-115616014	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1029470	chr5:115596277-115621603	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1017822	chr5:115596277-115625216	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv1019259	chr5:115596277-115625245	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv34342	chr5:115596277-115626966	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv2756234	chr5:115596277-115626966	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv432800	chr5:115596277-115626966	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1028323	chr5:115596277-115627008	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv1020633	chr5:115596277-115629523	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv1023495	chr5:115596277-115629769	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
32	esv2752575	chr5:115596277-115633474	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	nsv442961	chr5:115596334-115625228	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv1018649	chr5:115596350-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
35	nsv514321	chr5:115596461-115621213	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv1015300	chr5:115597953-115629523	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
37	nsv1028664	chr5:115601522-115630878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv1029334	chr5:115605092-115625245	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv10746	chr5:115609918-115617019	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
40	nsv1034438	chr5:115612225-115630878	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115611000-115615000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:115612000-115614200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:115612800-115633200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:115612800-115633200	Weak transcription	Ovary	ovary
5	chr5:115613400-115616800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:115613400-115628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:115613400-115641600	Weak transcription	HSMM	muscle
8	chr5:115613600-115615200	Weak transcription	Psoas Muscle	Psoas
9	chr5:115613600-115615400	Weak transcription	Liver	Liver
10	chr5:115613600-115616000	Weak transcription	Dnd41	blood
11	chr5:115613600-115619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:115613600-115621400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:115613600-115623200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:115613600-115623200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:115613600-115632000	Weak transcription	Fetal Heart	heart
16	chr5:115613600-115633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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