Variant report

Variant	rs12405915
Chromosome Location	chr1:245920921-245920922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12404746	1.00[AFR][1000 genomes]
rs1934564	1.00[AFR][1000 genomes]
rs28759401	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28833474	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28856014	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654082	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654083	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654084	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654085	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654111	1.00[AFR][1000 genomes]
rs4654189	0.97[AMR][1000 genomes]
rs58663870	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007728	chr1:245235174-246156455	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1002499	chr1:245365351-245929051	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497871	chr1:245706209-246655353	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv534412	chr1:245747724-246655416	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1003594	chr1:245801793-246649329	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv2752867	chr1:245829959-245932959	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004412	chr1:245830921-246169054	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv535385	chr1:245830921-246169054	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv873404	chr1:245850095-245964511	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006103	chr1:245881486-245968405	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv998007	chr1:245884759-245989362	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv949722	chr1:245898622-245997919	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1011255	chr1:245913512-246065050	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv468794	chr1:245914284-245999838	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv549520	chr1:245914284-245999838	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:245906400-245928400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:245908600-245925800	Weak transcription	HepG2	liver
3	chr1:245909800-245927600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:245910000-245932200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:245910200-245935200	Weak transcription	Ovary	ovary
6	chr1:245910400-245928400	Weak transcription	NHLF	lung
7	chr1:245910400-245934600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:245910800-245926600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:245911200-245935000	Weak transcription	Right Ventricle	heart
10	chr1:245911800-245924400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:245911800-245943600	Weak transcription	Dnd41	blood
12	chr1:245912000-245926000	Weak transcription	Gastric	stomach
13	chr1:245912000-245932400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:245912200-245928200	Weak transcription	Osteobl	bone
15	chr1:245912400-245925800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:245913200-245926800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:245915000-245925800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:245915400-245922400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:245915400-245927000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:245915600-245926000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:245915800-245928400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:245916200-245934800	Weak transcription	Fetal Stomach	stomach
23	chr1:245916400-245926800	Weak transcription	Fetal Heart	heart
24	chr1:245916400-245927200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:245916400-245930800	Weak transcription	Spleen	Spleen
26	chr1:245916400-245940000	Weak transcription	Left Ventricle	heart
27	chr1:245916800-245924000	Weak transcription	K562	blood
28	chr1:245917000-245930200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:245917000-245930600	Weak transcription	Lung	lung
30	chr1:245918400-245924600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:245918400-245933800	Weak transcription	Pancreas	Pancrea
32	chr1:245918600-245930200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:245920200-245933400	Weak transcription	Adipose Nuclei	Adipose
34	chr1:245920200-245934000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:245920600-245921000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:245920600-245925600	Weak transcription	Primary T cells from cord blood	blood

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