Variant report

Variant	rs4760665
Chromosome Location	chr12:49298503-49298504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:49296905-49298557	A549	lung:	n/a	n/a
2	CTCF	chr12:49298420-49298570	HFF-Myc	foreskin:	n/a	n/a
3	TCF12	chr12:49297553-49298642	A549	lung:	n/a	n/a
4	POLR2A	chr12:49298463-49298660	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49207912..49209568-chr12:49296260..49299188,2	K562	blood:
2	chr12:49258108..49259713-chr12:49297461..49298990,2	MCF-7	breast:
3	chr12:49258556..49260730-chr12:49298046..49299547,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239617	TF binding region
ENSG00000172602	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1051886	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054376	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747556	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747557	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747558	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783289	0.97[ASN][1000 genomes]
rs10783290	0.95[ASN][1000 genomes]
rs10783292	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783293	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10783294	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783295	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783297	0.91[ASN][1000 genomes]
rs10875886	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875888	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875893	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875894	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875895	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875896	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875897	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875898	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875900	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875901	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875902	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1111662	0.92[ASN][1000 genomes]
rs11168779	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168783	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168784	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168785	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168790	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168792	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168794	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168795	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168797	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168798	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168800	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168801	0.85[ASN][1000 genomes]
rs11168803	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168812	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11608916	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11610459	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610497	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11614474	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12227240	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228521	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229275	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12423542	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12579249	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1318692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1690182	0.89[ASN][1000 genomes]
rs1818996	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1830192	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2030900	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2070940	0.89[ASN][1000 genomes]
rs2073480	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131713	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272311	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2272312	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293449	0.94[ASN][1000 genomes]
rs2368701	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453063	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2463175	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2641450	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2694839	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2694840	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741627	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3759146	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782353	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825182	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3825184	0.99[ASN][1000 genomes]
rs4018510	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4237854	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433614	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4526804	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760600	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760647	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760661	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760662	0.83[EUR][1000 genomes]
rs4760663	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760664	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760666	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760667	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760668	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58023472	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59087236	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61941142	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61942166	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942167	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61942169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942207	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942209	0.81[ASN][1000 genomes]
rs6580696	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134686	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7297958	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7298330	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304942	0.98[ASN][1000 genomes]
rs7313988	0.90[ASN][1000 genomes]
rs7489036	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7963018	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963160	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976473	0.85[ASN][1000 genomes]
rs833820	0.89[ASN][1000 genomes]
rs833821	0.89[ASN][1000 genomes]
rs833822	0.90[ASN][1000 genomes]
rs833827	0.90[ASN][1000 genomes]
rs833828	0.88[ASN][1000 genomes]
rs833839	0.83[ASN][1000 genomes]
rs833840	0.83[ASN][1000 genomes]
rs833841	0.83[ASN][1000 genomes]
rs833842	0.83[ASN][1000 genomes]
rs961320	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9645813	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9783452	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9783477	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788029	0.95[ASN][1000 genomes]
rs9795742	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9796008	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4760665	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49297800-49298600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:49297800-49298600	Active TSS	Brain Angular Gyrus	brain
3	chr12:49298000-49298600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:49298000-49298600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:49298200-49298600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:49298200-49298600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:49298200-49298600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:49298200-49298600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:49298200-49298600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:49298200-49298600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr12:49298200-49298600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:49298200-49298600	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr12:49298200-49298600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:49298200-49298600	Bivalent Enhancer	Fetal Thymus	thymus
15	chr12:49298200-49298600	Enhancers	GM12878-XiMat	blood
16	chr12:49298200-49298600	Enhancers	HSMMtube	muscle
17	chr12:49298200-49298800	Active TSS	Fetal Brain Male	brain
18	chr12:49298200-49298800	Enhancers	Fetal Stomach	stomach
19	chr12:49298200-49298800	Enhancers	Gastric	stomach
20	chr12:49298200-49301000	Weak transcription	Liver	Liver
21	chr12:49298200-49315800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:49298200-49318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:49298400-49298600	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:49298400-49298600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:49298400-49298600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:49298400-49298600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:49298400-49298600	Enhancers	Adipose Nuclei	Adipose
28	chr12:49298400-49298600	Active TSS	Brain Anterior Caudate	brain
29	chr12:49298400-49298600	Flanking Active TSS	Fetal Kidney	kidney
30	chr12:49298400-49298600	Enhancers	Fetal Muscle Trunk	muscle
31	chr12:49298400-49298600	Active TSS	Stomach Smooth Muscle	stomach
32	chr12:49298400-49298600	Flanking Active TSS	A549	lung
33	chr12:49298400-49298600	Enhancers	HepG2	liver
34	chr12:49298400-49298800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:49298400-49298800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:49298400-49298800	Enhancers	Fetal Lung	lung
37	chr12:49298400-49298800	Enhancers	Fetal Muscle Leg	muscle
38	chr12:49298400-49298800	Enhancers	Pancreas	Pancrea
39	chr12:49298400-49299400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:49298400-49299800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:49298400-49301000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:49298400-49301000	Weak transcription	Fetal Intestine Small	intestine
43	chr12:49298400-49301000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:49298400-49301200	Weak transcription	Fetal Intestine Large	intestine
45	chr12:49298400-49308000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:49298400-49310400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:49298400-49310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:49298400-49310400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:49298400-49310600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:49298400-49310600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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