Variant report

Variant	rs17242777
Chromosome Location	chr12:105458257-105458258
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	chr12:105452142..105453731-chr12:105456982..105459077,2	K562	blood:
2	chr12:105446388..105448614-chr12:105457572..105460217,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10778366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861327	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10861328	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861329	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861330	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112347	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112349	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112350	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112351	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611105	0.82[ASN][1000 genomes]
rs11612252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613233	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11613261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196879	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1196880	0.90[ASN][1000 genomes]
rs1196882	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1196883	0.89[ASN][1000 genomes]
rs1196886	0.89[ASN][1000 genomes]
rs12367626	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732377	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2374451	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2440693	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4144467	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144468	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56118650	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56188643	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56369757	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61938827	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7308195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962686	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105409400-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr12:105413000-105476800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:105423200-105459400	Weak transcription	Lung	lung
5	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:105441200-105477000	Weak transcription	Gastric	stomach
8	chr12:105442400-105469800	Weak transcription	Fetal Lung	lung
9	chr12:105443400-105465000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:105445800-105472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:105447000-105461600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:105447000-105464600	Weak transcription	Left Ventricle	heart
13	chr12:105447000-105468000	Weak transcription	K562	blood
14	chr12:105447000-105468600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:105447200-105462000	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:105447200-105466800	Weak transcription	Brain Angular Gyrus	brain
17	chr12:105447200-105477200	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:105448200-105461400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:105448800-105459800	Weak transcription	Ovary	ovary
20	chr12:105448800-105461200	Strong transcription	Osteobl	bone
21	chr12:105449400-105476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:105450600-105461400	Strong transcription	HSMMtube	muscle
23	chr12:105450600-105461800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:105450800-105461400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:105450800-105468200	Weak transcription	Brain Anterior Caudate	brain
26	chr12:105451400-105458600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:105451600-105461400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:105452000-105461200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:105452000-105464200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:105452000-105466200	Weak transcription	GM12878-XiMat	blood
31	chr12:105452200-105458600	Weak transcription	NHDF-Ad	bronchial
32	chr12:105452200-105462000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:105453400-105460400	Strong transcription	Fetal Brain Female	brain
34	chr12:105453400-105476800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:105454200-105476600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:105454800-105459000	Strong transcription	Aorta	Aorta
37	chr12:105455000-105461400	Weak transcription	Spleen	Spleen
38	chr12:105455600-105465200	Strong transcription	HMEC	breast
39	chr12:105455600-105467800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:105455600-105476400	Weak transcription	Fetal Brain Male	brain
41	chr12:105456000-105477000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:105456200-105458400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:105456400-105475000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:105456600-105458400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:105456600-105463800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:105456600-105475200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:105456800-105458400	Weak transcription	Adipose Nuclei	Adipose
48	chr12:105456800-105458400	Weak transcription	Brain Germinal Matrix	brain
49	chr12:105456800-105458800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:105456800-105458800	Weak transcription	Fetal Muscle Leg	muscle

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