Variant report

Variant	rs9640279
Chromosome Location	chr7:150268098-150268099
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10085891	0.82[EUR][1000 genomes]
rs10216102	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10224387	0.86[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs10227094	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10235151	0.80[ASW][hapmap];0.82[CEU][hapmap]
rs10239578	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10240209	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10248553	0.84[EUR][1000 genomes]
rs10255487	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270122	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10273606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11971770	0.95[CEU][hapmap];0.86[CHB][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11975418	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11984138	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12671922	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1317276	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1916027	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2140138	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140139	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28537284	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28829297	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3088115	0.82[CEU][hapmap]
rs35890864	0.96[ASN][1000 genomes]
rs3735085	0.82[CEU][hapmap]
rs4143732	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55653011	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56158089	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57604196	0.86[EUR][1000 genomes]
rs60628216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464081	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6959171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959264	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6961075	0.94[EUR][1000 genomes]
rs73727323	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73727325	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73727338	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7781704	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7782221	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7787987	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7797456	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7800143	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7802869	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7806724	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs952642	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv3341786	chr7:150220353-150269134	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9640279	ZNF425	cis	cerebellum	SCAN
rs9640279	GIMAP4	cis	parietal	SCAN
rs9640279	HCA112	cis	multi-tissue	Pritchard
rs9640279	ZNF777	cis	parietal	SCAN
rs9640279	ATP6V0E2	cis	parietal	SCAN
rs9640279	LR8	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150264000-150268200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr7:150264400-150268200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr7:150265200-150271400	Weak transcription	Gastric	stomach
4	chr7:150265400-150269000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:150265600-150268200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
7	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:150266000-150268200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
9	chr7:150266200-150268600	Weak transcription	Fetal Intestine Large	intestine
10	chr7:150266200-150270600	Weak transcription	Thymus	Thymus
11	chr7:150266400-150268400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
12	chr7:150266600-150269000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:150266600-150269200	Weak transcription	Esophagus	oesophagus
14	chr7:150266600-150269200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:150266600-150269800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:150266800-150268200	Enhancers	Primary hematopoietic stem cells	blood
17	chr7:150266800-150268200	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
18	chr7:150266800-150268400	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:150266800-150268600	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
20	chr7:150267000-150268200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:150267000-150268400	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
22	chr7:150267000-150269600	Genic enhancers	HUVEC	blood vessel
23	chr7:150267000-150270600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:150267000-150271400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:150267000-150272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:150267200-150268200	Enhancers	Right Atrium	heart
27	chr7:150267200-150268400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr7:150267200-150268400	Genic enhancers	Placenta	Placenta
29	chr7:150267200-150268400	Genic enhancers	Spleen	Spleen
30	chr7:150267200-150268400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
31	chr7:150267200-150270000	ZNF genes & repeats	Lung	lung
32	chr7:150267200-150271400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:150267400-150268200	ZNF genes & repeats	Liver	Liver
34	chr7:150267400-150268400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
35	chr7:150267400-150269000	Strong transcription	Fetal Thymus	thymus
36	chr7:150267400-150269400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:150267400-150269800	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:150267600-150268200	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
39	chr7:150267600-150268200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
40	chr7:150267600-150268200	Strong transcription	Right Ventricle	heart
41	chr7:150267600-150269000	Weak transcription	Colonic Mucosa	Colon
42	chr7:150267600-150271000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:150267800-150268200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr7:150267800-150268200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr7:150267800-150268200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr7:150267800-150268400	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr7:150267800-150270200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr7:150267800-150278200	Weak transcription	Primary B cells from cord blood	blood
49	chr7:150268000-150268200	Strong transcription	Fetal Muscle Leg	muscle
50	chr7:150268000-150268200	Genic enhancers	Left Ventricle	heart

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