Variant report

Variant	rs2293172
Chromosome Location	chr7:150269542-150269543
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1110093	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11760959	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11760960	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11761391	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11762727	0.93[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs11765395	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11768988	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11769223	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11770957	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11771561	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11771962	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11772952	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11982681	0.94[EUR][1000 genomes]
rs12672072	0.94[EUR][1000 genomes]
rs12703077	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs12703078	0.92[EUR][1000 genomes]
rs12703083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13222905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13224067	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13231883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13232597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13240941	0.94[EUR][1000 genomes]
rs13242186	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs1568627	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs1568629	0.92[EUR][1000 genomes]
rs1860871	0.83[GIH][hapmap]
rs1916003	0.94[EUR][1000 genomes]
rs2177188	0.93[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2177189	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2286900	0.83[GIH][hapmap]
rs2293174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2373802	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34211617	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34514106	0.94[EUR][1000 genomes]
rs34545650	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35133885	0.94[EUR][1000 genomes]
rs35194540	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35225135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35388682	0.95[EUR][1000 genomes]
rs35496043	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35556724	0.89[EUR][1000 genomes]
rs35672177	0.94[EUR][1000 genomes]
rs35677477	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36021964	0.94[EUR][1000 genomes]
rs36159323	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36185661	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3735078	0.83[GIH][hapmap]
rs3735079	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs3807378	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4725345	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725348	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4725905	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs4725906	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs4725908	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4725921	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4725923	0.93[EUR][1000 genomes]
rs58414124	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62502270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62503177	0.94[EUR][1000 genomes]
rs6949485	0.94[EUR][1000 genomes]
rs73163503	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782113	0.94[EUR][1000 genomes]
rs7802853	0.94[EUR][1000 genomes]
rs7803234	0.94[EUR][1000 genomes]
rs7809438	0.94[EUR][1000 genomes]
rs9691508	0.85[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	esv16529	chr7:150249312-150312843	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2293172	ZNF425	cis	cerebellum	SCAN
rs2293172	MLL3	cis	parietal	SCAN
rs2293172	GIMAP4	cis	lymphoblastoid	seeQTL
rs2293172	TMEM176B	cis	cerebellum	SCAN
rs2293172	ATG9B	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150265200-150271400	Weak transcription	Gastric	stomach
2	chr7:150266200-150270600	Weak transcription	Thymus	Thymus
3	chr7:150266600-150269800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:150267000-150269600	Genic enhancers	HUVEC	blood vessel
5	chr7:150267000-150270600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:150267000-150271400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:150267000-150272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:150267200-150270000	ZNF genes & repeats	Lung	lung
9	chr7:150267200-150271400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:150267400-150269800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:150267600-150271000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:150267800-150270200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:150267800-150278200	Weak transcription	Primary B cells from cord blood	blood
14	chr7:150268000-150270000	Weak transcription	Small Intestine	intestine
15	chr7:150268000-150271400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:150268000-150271400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr7:150268000-150272000	Weak transcription	Brain Substantia Nigra	brain
18	chr7:150268200-150271000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr7:150268200-150271200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:150268200-150271400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
21	chr7:150268200-150271400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr7:150268200-150271600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
23	chr7:150268400-150270400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:150268400-150270400	Strong transcription	Placenta	Placenta
25	chr7:150268400-150271000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
26	chr7:150268400-150271200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr7:150268400-150271200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr7:150268400-150271400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
29	chr7:150268400-150271600	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr7:150268600-150270800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
31	chr7:150269000-150269800	Strong transcription	Colonic Mucosa	Colon
32	chr7:150269000-150270000	ZNF genes & repeats	Fetal Thymus	thymus
33	chr7:150269000-150270200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:150269000-150270400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
35	chr7:150269000-150271400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:150269200-150269800	Genic enhancers	Left Ventricle	heart
37	chr7:150269200-150269800	Genic enhancers	Spleen	Spleen
38	chr7:150269200-150270200	ZNF genes & repeats	Adipose Nuclei	Adipose
39	chr7:150269200-150270200	Weak transcription	Fetal Intestine Small	intestine
40	chr7:150269400-150269600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr7:150269400-150269600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr7:150269400-150269600	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr7:150269400-150269800	ZNF genes & repeats	Fetal Stomach	stomach
44	chr7:150269400-150269800	Strong transcription	Right Ventricle	heart
45	chr7:150269400-150269800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr7:150269400-150269800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
47	chr7:150269400-150270000	ZNF genes & repeats	Liver	Liver
48	chr7:150269400-150270200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr7:150269400-150270200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle

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