Variant report

Variant	rs1677405
Chromosome Location	chr5:115611377-115611378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115611187..115613784-chr5:115614610..115617269,2	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10042177	0.96[CEU][hapmap]
rs10051072	0.96[CEU][hapmap]
rs10051302	0.96[CEU][hapmap]
rs10056823	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10063312	0.95[CEU][hapmap]
rs10066081	0.96[CEU][hapmap]
rs10075063	1.00[CEU][hapmap]
rs10075195	1.00[CEU][hapmap]
rs10077013	0.92[CEU][hapmap]
rs10079176	1.00[CEU][hapmap]
rs10079466	0.96[CEU][hapmap]
rs10079691	0.95[CEU][hapmap]
rs10463453	0.82[CEU][hapmap]
rs1090077	0.84[EUR][1000 genomes]
rs11241352	0.83[CEU][hapmap]
rs11241374	0.95[CEU][hapmap]
rs11241375	0.92[CEU][hapmap]
rs1129494	1.00[CEU][hapmap]
rs1133187	1.00[CEU][hapmap]
rs11742938	0.96[CEU][hapmap]
rs12054994	0.91[CEU][hapmap]
rs12109104	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12657249	0.95[CEU][hapmap]
rs13157583	0.87[CEU][hapmap]
rs13159102	0.92[CEU][hapmap]
rs13161987	0.94[CEU][hapmap]
rs13172482	1.00[CEU][hapmap]
rs1382343	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1382344	0.93[EUR][1000 genomes]
rs1396478	1.00[CEU][hapmap]
rs1396481	0.96[CEU][hapmap]
rs1396482	0.96[CEU][hapmap]
rs149131	0.88[EUR][1000 genomes]
rs1508875	0.95[CEU][hapmap]
rs153593	0.88[EUR][1000 genomes]
rs153594	0.88[EUR][1000 genomes]
rs1567335	0.86[CEU][hapmap]
rs1588267	1.00[CEU][hapmap]
rs1644268	0.86[EUR][1000 genomes]
rs1669135	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1669136	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1677406	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs173813	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs253950	1.00[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253951	0.86[EUR][1000 genomes]
rs253952	0.87[EUR][1000 genomes]
rs253959	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs254171	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs254172	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs254173	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs254174	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs27125	0.88[EUR][1000 genomes]
rs37180	0.87[EUR][1000 genomes]
rs40192	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs41271	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs42959	0.91[EUR][1000 genomes]
rs6594938	1.00[CEU][hapmap]
rs6594948	0.96[CEU][hapmap]
rs6876901	1.00[CEU][hapmap]
rs6894046	0.85[CEU][hapmap]
rs6896479	1.00[CEU][hapmap]
rs712561	0.96[CEU][hapmap]
rs712591	0.84[EUR][1000 genomes]
rs712601	0.84[EUR][1000 genomes]
rs7723358	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7730551	1.00[CEU][hapmap]
rs7735539	0.95[CEU][hapmap]
rs784479	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs784481	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs785373	0.84[EUR][1000 genomes]
rs785375	0.82[EUR][1000 genomes]
rs803967	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs809188	0.84[EUR][1000 genomes]
rs809210	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs810742	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9326987	1.00[CEU][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	esv1795354	chr5:115609221-115612961	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
40	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1677405	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115599200-115612600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:115600600-115611400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:115604600-115613200	Weak transcription	Psoas Muscle	Psoas
4	chr5:115608800-115611600	Enhancers	Liver	Liver
5	chr5:115609200-115612000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:115610200-115611400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
7	chr5:115610800-115611800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr5:115610800-115613600	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr5:115611000-115612400	Weak transcription	Fetal Kidney	kidney
10	chr5:115611000-115615000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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