Variant report

Variant	rs1404424
Chromosome Location	chr7:17946604-17946605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:17946487..17949983-chr7:17978237..17982024,4	MCF-7	breast:
2	chr7:17945224..17947018-chr7:18012635..18015345,2	MCF-7	breast:
3	chr7:17945292..17946912-chr7:17947838..17950371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071189	Chromatin interaction

Extended variants
information (count: 167 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10216315	0.87[ASN][1000 genomes]
rs10227224	0.87[ASN][1000 genomes]
rs10227501	0.82[ASN][1000 genomes]
rs10227582	0.85[ASN][1000 genomes]
rs10231926	0.81[ASN][1000 genomes]
rs10249221	0.81[EUR][1000 genomes]
rs10264355	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10264445	0.84[EUR][1000 genomes]
rs10264447	0.83[EUR][1000 genomes]
rs10265373	0.87[ASN][1000 genomes]
rs1051603	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11768866	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11983260	0.86[ASN][1000 genomes]
rs12699918	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357796	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1404414	0.94[EUR][1000 genomes]
rs1404421	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1404422	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1404425	0.91[EUR][1000 genomes]
rs1524774	0.94[EUR][1000 genomes]
rs1524775	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524777	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1568815	0.89[ASN][1000 genomes]
rs1568817	0.90[ASN][1000 genomes]
rs1568818	0.90[ASN][1000 genomes]
rs1830006	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1852010	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1852011	0.89[EUR][1000 genomes]
rs1965534	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1997019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2030725	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2103144	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140710	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2177652	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254176	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2462512	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691552	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2691553	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691555	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691557	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691558	0.90[ASN][1000 genomes]
rs2691559	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691560	0.89[ASN][1000 genomes]
rs2691561	0.89[ASN][1000 genomes]
rs2691562	0.89[ASN][1000 genomes]
rs2691563	0.89[ASN][1000 genomes]
rs2691564	0.89[ASN][1000 genomes]
rs2691566	0.89[ASN][1000 genomes]
rs2691567	0.88[ASN][1000 genomes]
rs2691568	0.89[ASN][1000 genomes]
rs2691569	0.89[ASN][1000 genomes]
rs2691570	0.89[ASN][1000 genomes]
rs2691571	0.89[ASN][1000 genomes]
rs2691577	0.85[ASN][1000 genomes]
rs2691578	0.85[ASN][1000 genomes]
rs2691579	0.83[ASN][1000 genomes]
rs2691580	0.84[ASN][1000 genomes]
rs2691581	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691582	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691583	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691585	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691586	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691589	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691592	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691593	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691594	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691595	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691596	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2691597	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691600	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691601	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691602	0.94[EUR][1000 genomes]
rs2691604	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691605	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691607	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2691609	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691610	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691611	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2691612	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691613	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691615	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691616	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691617	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2691618	0.97[EUR][1000 genomes]
rs2691620	0.97[EUR][1000 genomes]
rs2691621	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691623	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2691625	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2691627	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691628	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691629	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691630	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2714855	0.85[ASN][1000 genomes]
rs2714857	0.87[ASN][1000 genomes]
rs2714859	0.90[ASN][1000 genomes]
rs2714860	0.89[ASN][1000 genomes]
rs2714861	0.89[ASN][1000 genomes]
rs2714863	0.89[ASN][1000 genomes]
rs2714864	0.89[ASN][1000 genomes]
rs2714865	0.89[ASN][1000 genomes]
rs2714866	0.89[ASN][1000 genomes]
rs2714867	0.89[ASN][1000 genomes]
rs2714868	0.89[ASN][1000 genomes]
rs2714869	0.90[ASN][1000 genomes]
rs2714870	0.89[ASN][1000 genomes]
rs2714875	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2714876	0.99[EUR][1000 genomes]
rs2714877	0.99[EUR][1000 genomes]
rs2723494	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723496	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723497	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723498	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723499	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723500	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723501	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723502	0.92[EUR][1000 genomes]
rs2723503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723504	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723505	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723506	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2723507	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2723508	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2723515	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723540	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2723545	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723552	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2723553	0.89[EUR][1000 genomes]
rs2723554	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2723555	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723556	0.94[EUR][1000 genomes]
rs2723562	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723567	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723569	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723570	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723571	0.97[EUR][1000 genomes]
rs2723572	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35819944	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4316058	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4532510	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4543433	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4719525	0.85[ASN][1000 genomes]
rs4721661	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4721665	0.98[EUR][1000 genomes]
rs4721671	0.83[ASN][1000 genomes]
rs56287412	0.89[ASN][1000 genomes]
rs67452591	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6953831	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6955984	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958131	0.86[EUR][1000 genomes]
rs6958211	0.86[EUR][1000 genomes]
rs6973480	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6978097	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6978103	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949451	0.87[EUR][1000 genomes]
rs9942602	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs998342	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1404424	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17900400-17956600	Weak transcription	A549	lung
2	chr7:17903600-17953000	Weak transcription	Thymus	Thymus
3	chr7:17903800-17949000	Weak transcription	NHEK	skin
4	chr7:17907200-17954800	Weak transcription	Spleen	Spleen
5	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:17913000-17955800	Weak transcription	K562	blood
7	chr7:17918200-17948000	Weak transcription	GM12878-XiMat	blood
8	chr7:17927200-17955000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr7:17928200-17946800	Weak transcription	Hela-S3	cervix
10	chr7:17929200-17951400	Weak transcription	Fetal Intestine Large	intestine
11	chr7:17929200-17952200	Weak transcription	Fetal Muscle Leg	muscle
12	chr7:17929800-17948000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:17929800-17949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:17929800-17951600	Weak transcription	Fetal Thymus	thymus
15	chr7:17929800-17954000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr7:17930000-17948200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:17930000-17949200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:17930000-17952400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:17930200-17946800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:17930200-17950200	Weak transcription	NHDF-Ad	bronchial
23	chr7:17930200-17951800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:17930200-17954200	Weak transcription	Placenta	Placenta
25	chr7:17934800-17949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:17936400-17947400	Weak transcription	Primary B cells from cord blood	blood
27	chr7:17938200-17951800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr7:17938800-17952800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr7:17940200-17950800	Weak transcription	Fetal Stomach	stomach
30	chr7:17940400-17947200	Weak transcription	Psoas Muscle	Psoas
31	chr7:17941000-17951600	Weak transcription	Right Ventricle	heart
32	chr7:17941000-17952400	Weak transcription	Ovary	ovary
33	chr7:17941200-17952400	Weak transcription	Gastric	stomach
34	chr7:17941400-17949200	Weak transcription	Fetal Intestine Small	intestine
35	chr7:17941400-17951000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:17941400-17958400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:17942600-17949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:17942800-17951800	Weak transcription	Left Ventricle	heart
39	chr7:17942800-17954800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:17942800-17954800	Weak transcription	Pancreas	Pancrea
41	chr7:17943200-17952400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:17943400-17946800	Weak transcription	HepG2	liver
43	chr7:17943400-17947600	Weak transcription	HMEC	breast
44	chr7:17943400-17951400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:17943800-17952400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:17943800-17956000	Weak transcription	Primary T cells from cord blood	blood
47	chr7:17944000-17953800	Weak transcription	Liver	Liver
48	chr7:17944000-17955400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr7:17944400-17947000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:17944600-17947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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