Variant report

Variant	rs1488691
Chromosome Location	chr1:92332865-92332866
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493856	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10875030	0.80[CHB][hapmap]
rs10875033	0.83[AMR][1000 genomes]
rs10875037	0.85[CHB][hapmap]
rs12124897	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12127774	0.80[CHB][hapmap]
rs12566180	0.85[CHB][hapmap]
rs12736904	0.93[CHB][hapmap]
rs2479871	0.85[CHB][hapmap]
rs4658278	0.99[ASN][1000 genomes]
rs6604060	0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6604061	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6656018	0.80[CHB][hapmap];0.80[CHD][hapmap];0.84[ASN][1000 genomes]
rs6680614	0.85[CHB][hapmap]
rs6684753	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7533784	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7550028	0.85[CHB][hapmap]
rs9661103	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
22	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv830581	chr1:92317207-92511175	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1488691	CDC7	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92296400-92335800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:92312000-92337200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:92317400-92337200	Weak transcription	K562	blood
4	chr1:92317400-92338000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:92317400-92344400	Weak transcription	Fetal Intestine Large	intestine
6	chr1:92317600-92335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:92318000-92336800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:92318000-92337000	Weak transcription	Small Intestine	intestine
9	chr1:92320000-92338000	Weak transcription	Lung	lung
10	chr1:92321800-92336800	Weak transcription	Right Atrium	heart
11	chr1:92325200-92335800	Weak transcription	Fetal Heart	heart
12	chr1:92326400-92335800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:92327200-92335000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:92330000-92335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:92330200-92334200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:92330400-92335800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:92330400-92335800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:92330400-92336800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:92330400-92337000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:92330400-92337600	Weak transcription	Fetal Kidney	kidney
21	chr1:92330400-92337800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:92330600-92334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:92330600-92335800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:92330600-92335800	Weak transcription	GM12878-XiMat	blood
25	chr1:92330600-92336200	Weak transcription	Fetal Thymus	thymus
26	chr1:92330600-92337000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:92330600-92337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:92330600-92337400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:92330800-92338000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:92330800-92338000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:92331600-92337800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:92331800-92333200	Enhancers	Colon Smooth Muscle	Colon
33	chr1:92331800-92334000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:92331800-92334000	Weak transcription	NHDF-Ad	bronchial
35	chr1:92332000-92333200	Enhancers	Adipose Nuclei	Adipose
36	chr1:92332000-92333200	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:92332200-92333000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:92332200-92333000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:92332200-92333000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:92332200-92333000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:92332200-92333200	Enhancers	Psoas Muscle	Psoas
42	chr1:92332200-92334200	Enhancers	Ovary	ovary
43	chr1:92332200-92335000	Genic enhancers	HepG2	liver
44	chr1:92332400-92333000	Enhancers	Fetal Stomach	stomach
45	chr1:92332400-92333000	Enhancers	Spleen	Spleen
46	chr1:92332400-92333200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:92332400-92333200	Enhancers	Placenta	Placenta
48	chr1:92332400-92333200	Enhancers	Left Ventricle	heart
49	chr1:92332400-92334400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:92332400-92335800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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