Variant report

Variant	rs1192529
Chromosome Location	chr1:92256660-92256661
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	chr1:92252697..92255267-chr1:92255906..92257431,2	K562	blood:
2	chr1:92243502..92246899-chr1:92255853..92258486,3	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11165556	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11165595	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165637	0.83[EUR][1000 genomes]
rs1192528	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12043241	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12726500	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2489188	0.82[MEX][hapmap]
rs2810904	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs284139	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs284140	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs284142	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs284143	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs284144	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs284147	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284149	0.93[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284152	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs284153	0.82[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284154	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs284159	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs284167	0.83[EUR][1000 genomes]
rs416624	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7555476	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7555548	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

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
rs1192529	KCNV1	trans	cerebellum	SCAN
rs1192529	GBP7	cis	parietal	SCAN
rs1192529	GFI1	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92227000-92257200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:92233200-92257000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:92244600-92257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:92245200-92261200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:92245600-92258400	Weak transcription	Brain Angular Gyrus	brain
6	chr1:92246800-92257800	Genic enhancers	NHDF-Ad	bronchial
7	chr1:92248200-92268800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:92248600-92262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:92248600-92268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:92249000-92256800	Weak transcription	Small Intestine	intestine
11	chr1:92249000-92257200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:92249000-92257200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:92249000-92257200	Weak transcription	Esophagus	oesophagus
14	chr1:92249200-92256800	Weak transcription	Pancreas	Pancrea
15	chr1:92249200-92257000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:92249200-92263800	Weak transcription	Aorta	Aorta
17	chr1:92250400-92263800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:92250600-92256800	Weak transcription	Psoas Muscle	Psoas
19	chr1:92253200-92257400	Enhancers	Colon Smooth Muscle	Colon
20	chr1:92253200-92263600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:92253800-92257000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:92253800-92259400	Enhancers	Fetal Kidney	kidney
23	chr1:92254000-92257000	Weak transcription	Right Atrium	heart
24	chr1:92254000-92257000	Weak transcription	Right Ventricle	heart
25	chr1:92254000-92257000	Weak transcription	Spleen	Spleen
26	chr1:92254000-92257200	Enhancers	Fetal Stomach	stomach
27	chr1:92254000-92257200	Weak transcription	Lung	lung
28	chr1:92254000-92257600	Enhancers	Stomach Smooth Muscle	stomach
29	chr1:92254000-92258200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:92254000-92259000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:92254000-92269400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:92254400-92257000	Weak transcription	Adipose Nuclei	Adipose
33	chr1:92254400-92257800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:92254600-92259200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:92255000-92258000	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:92255000-92258000	Weak transcription	HUVEC	blood vessel
37	chr1:92255000-92258800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:92255000-92259000	Enhancers	Fetal Heart	heart
39	chr1:92255200-92256800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:92255200-92257200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:92255200-92258600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:92255200-92258600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr1:92255200-92258600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:92255400-92256800	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:92255400-92257000	Weak transcription	Liver	Liver
46	chr1:92255400-92257200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:92255400-92257200	Weak transcription	Ovary	ovary
48	chr1:92255400-92257400	Weak transcription	NHLF	lung
49	chr1:92255400-92258200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:92255400-92258800	Enhancers	Fetal Lung	lung

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