Variant report

Variant	rs2691574
Chromosome Location	chr7:17955025-17955026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10216315	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs10227224	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10227501	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.91[EUR][1000 genomes]
rs10227582	0.96[CEU][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap]
rs10231926	0.89[EUR][1000 genomes]
rs10233816	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10265373	0.96[CEU][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap]
rs10447542	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11973277	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11983260	0.88[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12699919	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1568815	0.96[CEU][hapmap];0.91[YRI][hapmap]
rs1568817	0.96[CEU][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap]
rs2691560	0.81[AMR][1000 genomes]
rs2691561	0.92[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs2691562	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2691563	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2691564	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2691566	0.96[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2691567	0.80[AFR][1000 genomes]
rs2691568	0.81[AFR][1000 genomes]
rs2691569	0.80[AFR][1000 genomes]
rs2691570	0.96[CEU][hapmap];0.80[AFR][1000 genomes]
rs2691571	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2691572	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2691573	0.85[AMR][1000 genomes]
rs2691575	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2691576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2691577	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691578	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691579	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2691580	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2714853	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2714854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2714855	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2714856	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2714857	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2714858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2714859	0.96[CEU][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs2714862	1.00[CHB][hapmap]
rs2714863	0.83[AFR][1000 genomes]
rs2714864	0.85[JPT][hapmap];0.87[YRI][hapmap]
rs2714865	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2714866	0.96[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs2714867	0.96[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2714868	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs2714869	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs2714870	0.96[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap]
rs2714878	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs2723541	0.94[CHB][hapmap]
rs4721670	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4721671	0.85[JPT][hapmap]
rs6952907	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6962380	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7802343	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes];0.88[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
rs2691574	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17900400-17956600	Weak transcription	A549	lung
2	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:17913000-17955800	Weak transcription	K562	blood
4	chr7:17941400-17958400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:17943800-17956000	Weak transcription	Primary T cells from cord blood	blood
6	chr7:17944000-17955400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr7:17944800-17955200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:17947000-17955200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:17947200-17955400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:17947400-17956600	Weak transcription	Fetal Lung	lung
11	chr7:17947400-17957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:17948200-17961000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:17948400-17960800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:17948600-17962800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:17950600-17955800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:17950800-17956800	Weak transcription	Primary B cells from cord blood	blood
17	chr7:17951600-17956600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:17952800-17955400	Enhancers	Brain Hippocampus Middle	brain
19	chr7:17952800-17964400	Weak transcription	Gastric	stomach
20	chr7:17953000-17955400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:17953000-17961600	Weak transcription	Aorta	Aorta
22	chr7:17953000-17963000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:17953200-17955200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:17953200-17960600	Weak transcription	Fetal Heart	heart
25	chr7:17953200-17960600	Weak transcription	Right Ventricle	heart
26	chr7:17953200-17964600	Weak transcription	Esophagus	oesophagus
27	chr7:17953600-17955200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:17953600-17955400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr7:17953600-17955600	Enhancers	HepG2	liver
30	chr7:17953800-17955200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:17953800-17955600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr7:17953800-17955600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr7:17954200-17955200	Enhancers	Placenta	Placenta
34	chr7:17954200-17955400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr7:17954200-17955400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr7:17954200-17955600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr7:17954400-17955200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:17954400-17955200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:17954600-17955200	Weak transcription	Brain Anterior Caudate	brain
40	chr7:17954600-17957600	Weak transcription	Liver	Liver
41	chr7:17954800-17955200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr7:17954800-17955200	Enhancers	Left Ventricle	heart
43	chr7:17954800-17955200	Enhancers	Ovary	ovary
44	chr7:17954800-17955200	Enhancers	Pancreas	Pancrea
45	chr7:17954800-17955200	Enhancers	Right Atrium	heart
46	chr7:17954800-17955400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr7:17954800-17955400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:17954800-17955400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr7:17954800-17955400	Enhancers	Lung	lung
50	chr7:17954800-17955400	Enhancers	Psoas Muscle	Psoas

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