Variant report

Variant	rs12507173
Chromosome Location	chr4:69923543-69923544
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10000598	0.80[EUR][1000 genomes]
rs10006282	0.80[EUR][1000 genomes]
rs10010699	0.80[EUR][1000 genomes]
rs10025070	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10033045	0.93[ASN][1000 genomes]
rs10518057	0.80[EUR][1000 genomes]
rs10903224	0.80[EUR][1000 genomes]
rs11931604	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11932983	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933432	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11936412	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11937195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11945620	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11945705	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11946976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12499093	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12499192	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12503622	0.82[ASN][1000 genomes]
rs12506592	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12507556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508920	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12509040	0.86[EUR][1000 genomes]
rs13132528	0.80[EUR][1000 genomes]
rs13136922	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13148603	0.80[EUR][1000 genomes]
rs1379813	0.80[EUR][1000 genomes]
rs1379816	0.80[EUR][1000 genomes]
rs1458245	0.80[EUR][1000 genomes]
rs1458246	0.80[EUR][1000 genomes]
rs1598904	0.80[EUR][1000 genomes]
rs17605102	0.85[EUR][1000 genomes]
rs1841052	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1993546	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2125307	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365062	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34545777	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34561399	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4259121	0.93[ASN][1000 genomes]
rs4343788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4348159	0.87[ASN][1000 genomes]
rs4418041	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434329	0.93[ASN][1000 genomes]
rs4554146	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694152	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694550	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694606	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55676022	0.82[ASN][1000 genomes]
rs55831171	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55905314	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56943005	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57468707	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58965335	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59314351	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59732068	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60276248	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62296919	0.93[ASN][1000 genomes]
rs62296937	0.84[EUR][1000 genomes]
rs62296941	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62298861	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62298872	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66698711	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72642933	0.84[EUR][1000 genomes]
rs72642938	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72642947	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72642961	0.93[ASN][1000 genomes]
rs7435335	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7441753	0.80[EUR][1000 genomes]
rs7680341	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7692753	0.81[EUR][1000 genomes]
rs9991142	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69919600-69924000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:69922600-69925000	Enhancers	Fetal Intestine Large	intestine
3	chr4:69922800-69923600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:69922800-69923600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:69922800-69924000	Enhancers	HSMMtube	muscle
6	chr4:69922800-69924200	Enhancers	HSMM	muscle
7	chr4:69922800-69924800	Flanking Active TSS	Liver	Liver
8	chr4:69922800-69925000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr4:69923000-69923600	Flanking Active TSS	GM12878-XiMat	blood
10	chr4:69923000-69923800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:69923000-69923800	Active TSS	Fetal Kidney	kidney
12	chr4:69923000-69924000	Enhancers	A549	lung
13	chr4:69923000-69924600	Flanking Active TSS	HepG2	liver
14	chr4:69923000-69924800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:69923200-69923600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:69923200-69923800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:69923200-69923800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:69923200-69923800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:69923200-69923800	Active TSS	Brain Hippocampus Middle	brain
20	chr4:69923200-69923800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr4:69923200-69923800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:69923200-69923800	Enhancers	HMEC	breast
23	chr4:69923200-69924000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:69923200-69924000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr4:69923200-69924000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:69923200-69924000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:69923200-69924000	Active TSS	Duodenum Mucosa	Duodenum
28	chr4:69923200-69924000	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr4:69923200-69924200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:69923200-69924200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:69923200-69924600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr4:69923200-69924800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr4:69923200-69925000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:69923400-69923600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:69923400-69923600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:69923400-69923600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:69923400-69923600	Active TSS	Brain Anterior Caudate	brain
38	chr4:69923400-69923800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr4:69923400-69923800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:69923400-69923800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:69923400-69923800	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr4:69923400-69923800	Active TSS	Brain Cingulate Gyrus	brain
43	chr4:69923400-69923800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:69923400-69923800	Active TSS	Colonic Mucosa	Colon
45	chr4:69923400-69923800	Active TSS	Fetal Intestine Small	intestine
46	chr4:69923400-69923800	Active TSS	Pancreas	Pancrea
47	chr4:69923400-69923800	Active TSS	Rectal Smooth Muscle	rectum
48	chr4:69923400-69923800	Active TSS	Stomach Mucosa	stomach
49	chr4:69923400-69923800	Active TSS	Osteobl	bone
50	chr4:69923400-69924000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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