Variant report

Variant	rs12699919
Chromosome Location	chr7:17972026-17972027
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	chr7:17965161..17967568-chr7:17969266..17972579,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10216315	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs10227224	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10227501	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10227582	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10231926	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10233816	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10265373	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs10447542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11973277	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11983260	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs1568815	0.96[CEU][hapmap]
rs1568817	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2691561	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs2691562	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2691564	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2691566	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2691570	0.96[CEU][hapmap]
rs2691572	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691573	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2691574	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2691575	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691576	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691577	0.97[EUR][1000 genomes]
rs2691578	0.97[EUR][1000 genomes]
rs2691579	0.96[EUR][1000 genomes]
rs2691580	1.00[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs2714853	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2714855	1.00[CEU][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes]
rs2714856	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2714857	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2714858	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2714859	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2714862	0.91[CHB][hapmap]
rs2714864	0.87[JPT][hapmap]
rs2714866	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2714867	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs2714868	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs2714869	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs2714870	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs2714878	0.96[CEU][hapmap]
rs2723541	0.96[CHB][hapmap]
rs4721670	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4721671	0.86[JPT][hapmap]
rs6952907	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6962380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7802343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv531013	chr7:17970218-18248642	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12699919	SNX13	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:17955000-17977400	Weak transcription	Fetal Intestine Small	intestine
3	chr7:17955400-17973000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:17959600-17972800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:17961800-17977400	Weak transcription	Brain Angular Gyrus	brain
6	chr7:17961800-17978800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:17962000-17973400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:17962000-17975800	Weak transcription	Hela-S3	cervix
9	chr7:17962200-17973200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:17962200-17977400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:17962400-17978600	Weak transcription	Aorta	Aorta
12	chr7:17963400-17972400	Weak transcription	Right Ventricle	heart
13	chr7:17963400-17977000	Weak transcription	Fetal Lung	lung
14	chr7:17963400-17977400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:17963800-17977800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:17965400-17977200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:17966600-17974800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr7:17967000-17972400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:17967200-17972800	Weak transcription	Spleen	Spleen
20	chr7:17967200-17978800	Weak transcription	Lung	lung
21	chr7:17968200-17972200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:17968200-17973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:17968800-17975200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:17969200-17977800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr7:17969600-17973400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:17970400-17973600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:17970600-17972200	Enhancers	Fetal Heart	heart
28	chr7:17970600-17972400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:17970600-17972800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr7:17970600-17972800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr7:17970600-17973000	Enhancers	Liver	Liver
32	chr7:17970600-17973400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:17970600-17974000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:17970600-17974200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:17970600-17977400	Weak transcription	Ovary	ovary
36	chr7:17970600-17978800	Weak transcription	Pancreas	Pancrea
37	chr7:17970800-17972400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:17970800-17973600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:17970800-17974400	Weak transcription	HepG2	liver
40	chr7:17970800-17974800	Weak transcription	Psoas Muscle	Psoas
41	chr7:17970800-17977400	Weak transcription	Adipose Nuclei	Adipose
42	chr7:17970800-17977400	Weak transcription	Right Atrium	heart
43	chr7:17970800-17978000	Weak transcription	Left Ventricle	heart
44	chr7:17970800-17978600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:17970800-17978800	Weak transcription	Gastric	stomach
46	chr7:17971000-17972400	Weak transcription	GM12878-XiMat	blood
47	chr7:17971000-17977200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:17971000-17977400	Weak transcription	NHDF-Ad	bronchial
49	chr7:17971200-17972200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr7:17971200-17973200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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