Variant report

Variant	rs2714876
Chromosome Location	chr7:17927606-17927607
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:17921608..17923837-chr7:17925964..17929723,3	MCF-7	breast:

Extended variants
information (count: 130 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10249221	0.81[EUR][1000 genomes]
rs10264355	0.91[EUR][1000 genomes]
rs10264445	0.84[EUR][1000 genomes]
rs10264447	0.83[EUR][1000 genomes]
rs1051603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs11768866	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12699918	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1357796	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1404414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1404421	0.90[EUR][1000 genomes]
rs1404422	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1404424	0.99[EUR][1000 genomes]
rs1404425	0.91[EUR][1000 genomes]
rs1524774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1524775	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1524776	1.00[CEU][hapmap]
rs1524777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1830006	0.91[EUR][1000 genomes]
rs1852010	0.91[EUR][1000 genomes]
rs1852011	0.89[EUR][1000 genomes]
rs1965534	0.91[EUR][1000 genomes]
rs1997019	0.91[EUR][1000 genomes]
rs2030725	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2103144	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2140710	0.98[EUR][1000 genomes]
rs2177652	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2254176	0.91[EUR][1000 genomes]
rs2389858	0.90[CEU][hapmap]
rs2462512	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691552	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2691553	0.91[EUR][1000 genomes]
rs2691555	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691557	0.99[EUR][1000 genomes]
rs2691559	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691581	0.91[EUR][1000 genomes]
rs2691582	0.91[EUR][1000 genomes]
rs2691583	0.92[CEU][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs2691585	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691586	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2691589	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691592	0.90[EUR][1000 genomes]
rs2691593	0.90[EUR][1000 genomes]
rs2691594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2691595	0.90[EUR][1000 genomes]
rs2691596	0.90[EUR][1000 genomes]
rs2691597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691600	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2691601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2691602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691604	0.91[EUR][1000 genomes]
rs2691605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2691607	0.97[EUR][1000 genomes]
rs2691609	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2691610	0.91[EUR][1000 genomes]
rs2691611	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2691612	1.00[CEU][hapmap];0.87[YRI][hapmap];0.98[EUR][1000 genomes]
rs2691613	0.98[EUR][1000 genomes]
rs2691615	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2691616	0.91[EUR][1000 genomes]
rs2691617	0.84[EUR][1000 genomes]
rs2691618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691621	0.91[EUR][1000 genomes]
rs2691623	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691625	0.89[EUR][1000 genomes]
rs2691627	0.91[EUR][1000 genomes]
rs2691628	0.91[EUR][1000 genomes]
rs2691629	0.91[EUR][1000 genomes]
rs2691630	0.91[EUR][1000 genomes]
rs2714875	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2714877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2714878	0.85[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2723494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723496	0.91[EUR][1000 genomes]
rs2723497	0.91[EUR][1000 genomes]
rs2723498	0.91[EUR][1000 genomes]
rs2723499	0.91[EUR][1000 genomes]
rs2723500	0.91[EUR][1000 genomes]
rs2723501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2723503	0.91[EUR][1000 genomes]
rs2723504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723506	0.90[EUR][1000 genomes]
rs2723507	0.90[EUR][1000 genomes]
rs2723508	0.90[EUR][1000 genomes]
rs2723515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723540	1.00[CEU][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723545	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2723552	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs2723553	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723554	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2723555	0.92[EUR][1000 genomes]
rs2723556	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723562	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723567	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2723569	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723570	0.98[EUR][1000 genomes]
rs2723571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2723572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35819944	0.98[EUR][1000 genomes]
rs4316058	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4532510	0.97[EUR][1000 genomes]
rs4543433	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4721661	0.95[EUR][1000 genomes]
rs4721665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4721666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap]
rs67452591	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953831	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6955984	0.88[EUR][1000 genomes]
rs6958131	0.85[EUR][1000 genomes]
rs6958211	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6973480	0.96[CEU][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs6978097	0.89[EUR][1000 genomes]
rs6978103	0.87[EUR][1000 genomes]
rs949451	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9942602	0.84[EUR][1000 genomes]
rs998342	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869352	chr7:17237983-17932878	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv534309	chr7:17254118-17932878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv887808	chr7:17920613-18150005	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1018517	chr7:17926468-18127372	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2714876	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17839000-17932600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:17885000-17928800	Weak transcription	HUVEC	blood vessel
3	chr7:17885200-17933800	Weak transcription	HMEC	breast
4	chr7:17888400-17934800	Weak transcription	Colonic Mucosa	Colon
5	chr7:17895000-17933600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr7:17900400-17956600	Weak transcription	A549	lung
7	chr7:17901400-17946200	Weak transcription	NHLF	lung
8	chr7:17901600-17939800	Weak transcription	Pancreas	Pancrea
9	chr7:17903400-17930000	Weak transcription	Gastric	stomach
10	chr7:17903400-17942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:17903600-17945400	Weak transcription	Aorta	Aorta
12	chr7:17903600-17953000	Weak transcription	Thymus	Thymus
13	chr7:17903800-17949000	Weak transcription	NHEK	skin
14	chr7:17905200-17928400	Weak transcription	NHDF-Ad	bronchial
15	chr7:17906400-17937800	Weak transcription	Brain Angular Gyrus	brain
16	chr7:17906400-17937800	Weak transcription	Brain Anterior Caudate	brain
17	chr7:17907200-17931400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:17907200-17931600	Weak transcription	Fetal Brain Male	brain
19	chr7:17907200-17937800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:17907200-17939800	Weak transcription	Lung	lung
21	chr7:17907200-17941000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr7:17907200-17954800	Weak transcription	Spleen	Spleen
23	chr7:17907400-17942400	Weak transcription	Small Intestine	intestine
24	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:17911600-17942400	Weak transcription	HepG2	liver
26	chr7:17911800-17928800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:17911800-17933200	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:17911800-17939800	Weak transcription	Psoas Muscle	Psoas
29	chr7:17911800-17942400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:17912400-17932200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:17912400-17939800	Weak transcription	Right Ventricle	heart
32	chr7:17913000-17928000	Weak transcription	HSMMtube	muscle
33	chr7:17913000-17937800	Weak transcription	Brain Substantia Nigra	brain
34	chr7:17913000-17955800	Weak transcription	K562	blood
35	chr7:17915400-17928200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr7:17916200-17942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:17918200-17948000	Weak transcription	GM12878-XiMat	blood
38	chr7:17918600-17932200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr7:17918600-17936600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr7:17918600-17938000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:17918800-17942600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:17919000-17930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr7:17919000-17931600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr7:17919200-17934400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr7:17919400-17929200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:17920200-17929800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr7:17920200-17930400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:17921600-17934600	Weak transcription	Osteobl	bone
49	chr7:17922000-17927800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr7:17922200-17929800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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