Variant report

Variant	rs428815
Chromosome Location	chr1:92260920-92260921
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92259196..92261708-chr1:92278967..92281416,2	K562	blood:
2	chr1:92258357..92261493-chr1:92263209..92266078,3	K562	blood:
3	chr1:92258357..92261637-chr1:92263209..92266078,4	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1032255	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.88[YRI][hapmap]
rs10874980	1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs11799400	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12027931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1352438	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs1805109	0.82[ASW][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs1805110	0.82[ASW][hapmap];1.00[TSI][hapmap]
rs2129972	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs2129973	0.88[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap]
rs2391070	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs2489178	0.81[JPT][hapmap]
rs2489186	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs2489189	0.82[ASW][hapmap]
rs2634028	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs2634030	0.82[ASW][hapmap];1.00[TSI][hapmap]
rs2634034	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs2634036	0.88[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap]
rs2799512	0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2799516	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs2799522	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs2799524	1.00[TSI][hapmap]
rs2799539	0.87[JPT][hapmap]
rs2799547	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs284141	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284148	0.88[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs284160	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs284161	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs284162	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs284163	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs284164	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs3103332	0.88[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap]
rs449960	1.00[CEU][hapmap]
rs717923	0.87[JPT][hapmap];0.88[YRI][hapmap]
rs7550856	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901913	0.88[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs901917	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs428815	EPHX4	cis	cerebellum	SCAN
rs428815	RPL5	cis	cerebellum	SCAN
rs428815	GLMN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92245200-92261200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:92248200-92268800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:92248600-92262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:92248600-92268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:92249200-92263800	Weak transcription	Aorta	Aorta
6	chr1:92250400-92263800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:92253200-92263600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:92254000-92269400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:92257600-92264000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:92257600-92279400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:92257800-92261000	Weak transcription	Liver	Liver
12	chr1:92257800-92262800	Weak transcription	Lung	lung
13	chr1:92257800-92269600	Weak transcription	A549	lung
14	chr1:92258000-92261400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:92258000-92261400	Weak transcription	Right Atrium	heart
16	chr1:92258000-92262800	Weak transcription	Spleen	Spleen
17	chr1:92258000-92263800	Weak transcription	Esophagus	oesophagus
18	chr1:92258000-92264600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:92258000-92268400	Weak transcription	Fetal Thymus	thymus
20	chr1:92258200-92263800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:92258200-92269400	Weak transcription	Hela-S3	cervix
22	chr1:92258400-92264000	Weak transcription	Pancreas	Pancrea
23	chr1:92258400-92264400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:92258400-92264600	Weak transcription	Fetal Intestine Large	intestine
25	chr1:92258400-92271400	Weak transcription	Fetal Intestine Small	intestine
26	chr1:92258600-92261200	Weak transcription	Left Ventricle	heart
27	chr1:92258600-92262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:92258600-92262600	Weak transcription	Right Ventricle	heart
29	chr1:92258600-92263000	Weak transcription	Brain Angular Gyrus	brain
30	chr1:92258600-92263600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:92258600-92263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:92258600-92263600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:92258600-92263800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:92258600-92263800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:92258600-92263800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:92258600-92263800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:92258600-92264000	Weak transcription	Brain Anterior Caudate	brain
38	chr1:92258600-92264600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:92258600-92268600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:92258600-92270000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:92258800-92261000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:92258800-92261000	Weak transcription	K562	blood
43	chr1:92258800-92263600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:92258800-92272400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:92259000-92262600	Weak transcription	Ovary	ovary
46	chr1:92259000-92263800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:92259000-92264400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:92259200-92261000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:92259200-92261600	Weak transcription	Placenta	Placenta
50	chr1:92259600-92263000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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