Variant report

Variant	rs1568815
Chromosome Location	chr7:17943345-17943346
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr7:17943059-17943539	MCF-7	breast:	n/a	n/a
2	GATA3	chr7:17943337-17943765	SH-SY5Y	brain:	n/a	n/a
3	CEBPB	chr7:17942954-17943406	MCF-7	breast:	n/a	chr7:17943237-17943250
4	ARID3A	chr7:17943025-17943444	HepG2	liver:	n/a	n/a
5	EP300	chr7:17943071-17943348	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:17941921..17944497-chr7:17966021..17968110,2	K562	blood:
2	chr7:17910600..17912599-chr7:17942019..17944192,2	K562	blood:

Variant related genes	Relation type
SNX13	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10216315	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10227224	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10227501	0.96[CEU][hapmap];0.91[ASN][1000 genomes]
rs10227582	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10231926	0.91[ASN][1000 genomes]
rs10233816	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs10265373	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10447542	0.96[CEU][hapmap]
rs11768866	0.87[ASN][1000 genomes]
rs11973277	0.96[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs11983260	0.92[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12699918	0.87[ASN][1000 genomes]
rs12699919	0.96[CEU][hapmap]
rs1404424	0.89[ASN][1000 genomes]
rs1464804	0.88[ASN][1000 genomes]
rs1524775	0.89[ASN][1000 genomes]
rs1568817	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568818	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2103144	0.90[ASN][1000 genomes]
rs2177652	0.81[ASN][1000 genomes]
rs2691555	0.89[ASN][1000 genomes]
rs2691557	0.89[ASN][1000 genomes]
rs2691558	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691559	0.89[ASN][1000 genomes]
rs2691560	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691561	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691562	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691563	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691564	1.00[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691565	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691566	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691567	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691568	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691569	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691570	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691571	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691572	0.92[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs2691574	0.96[CEU][hapmap];0.91[YRI][hapmap]
rs2691576	0.96[CEU][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs2691577	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2691578	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2691579	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2691580	0.96[CEU][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2714853	0.83[AMR][1000 genomes]
rs2714854	0.96[CEU][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs2714855	0.96[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2714856	0.84[AMR][1000 genomes]
rs2714857	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714858	0.96[CEU][hapmap];0.83[YRI][hapmap]
rs2714859	1.00[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714860	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714861	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714863	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714864	1.00[ASN][1000 genomes]
rs2714865	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714866	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714867	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714868	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714869	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2714870	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2714871	0.86[ASN][1000 genomes]
rs2714872	0.89[ASN][1000 genomes]
rs2714878	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2723540	0.83[ASN][1000 genomes]
rs35819944	0.86[ASN][1000 genomes]
rs4532510	0.87[ASN][1000 genomes]
rs4543433	0.87[ASN][1000 genomes]
rs4719525	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4721671	0.94[ASN][1000 genomes]
rs6952907	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs6955984	0.84[ASN][1000 genomes]
rs6962380	0.96[CEU][hapmap]
rs6973480	0.82[ASN][1000 genomes]
rs7802343	0.96[CEU][hapmap]
rs9942602	0.84[ASN][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
rs1568815	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17900400-17956600	Weak transcription	A549	lung
2	chr7:17901400-17946200	Weak transcription	NHLF	lung
3	chr7:17903600-17945400	Weak transcription	Aorta	Aorta
4	chr7:17903600-17953000	Weak transcription	Thymus	Thymus
5	chr7:17903800-17949000	Weak transcription	NHEK	skin
6	chr7:17907200-17954800	Weak transcription	Spleen	Spleen
7	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:17913000-17955800	Weak transcription	K562	blood
9	chr7:17918200-17948000	Weak transcription	GM12878-XiMat	blood
10	chr7:17927200-17944600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr7:17927200-17955000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:17928200-17946800	Weak transcription	Hela-S3	cervix
13	chr7:17929200-17951400	Weak transcription	Fetal Intestine Large	intestine
14	chr7:17929200-17952200	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:17929800-17943400	Weak transcription	Primary T cells from cord blood	blood
16	chr7:17929800-17944200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:17929800-17946600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:17929800-17948000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:17929800-17949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:17929800-17951600	Weak transcription	Fetal Thymus	thymus
21	chr7:17929800-17954000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:17930000-17948200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:17930000-17949200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:17930000-17952400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:17930200-17946800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:17930200-17950200	Weak transcription	NHDF-Ad	bronchial
29	chr7:17930200-17951800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:17930200-17954200	Weak transcription	Placenta	Placenta
31	chr7:17932200-17946200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr7:17934800-17949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:17936400-17947400	Weak transcription	Primary B cells from cord blood	blood
34	chr7:17938200-17944000	Weak transcription	Brain Anterior Caudate	brain
35	chr7:17938200-17951800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:17938800-17952800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:17940200-17950800	Weak transcription	Fetal Stomach	stomach
38	chr7:17940400-17947200	Weak transcription	Psoas Muscle	Psoas
39	chr7:17941000-17943400	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr7:17941000-17943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:17941000-17951600	Weak transcription	Right Ventricle	heart
42	chr7:17941000-17952400	Weak transcription	Ovary	ovary
43	chr7:17941200-17944200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr7:17941200-17944200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr7:17941200-17944200	Weak transcription	Esophagus	oesophagus
46	chr7:17941200-17944800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:17941200-17952400	Weak transcription	Gastric	stomach
48	chr7:17941400-17943800	Weak transcription	Right Atrium	heart
49	chr7:17941400-17949200	Weak transcription	Fetal Intestine Small	intestine
50	chr7:17941400-17951000	Weak transcription	Monocytes-CD14+_RO01746	blood

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