Variant report

Variant	rs2641450
Chromosome Location	chr12:49341386-49341387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49329355..49335445-chr12:49337368..49342700,9	MCF-7	breast:
2	chr12:49216823..49218627-chr12:49340038..49341601,2	K562	blood:
3	chr12:49338699..49342027-chr12:49368577..49371110,3	MCF-7	breast:
4	chr12:49333826..49338604-chr12:49339041..49343164,6	K562	blood:
5	chr12:49339279..49342706-chr12:49347580..49351500,3	K562	blood:
6	chr12:49335913..49337732-chr12:49340843..49342555,2	K562	blood:

Variant related genes	Relation type
ENSG00000272822	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000255863	Chromatin interaction
ENSG00000200303	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1051886	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1054376	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747556	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10747557	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747558	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783289	0.86[ASN][1000 genomes]
rs10783290	0.83[ASN][1000 genomes]
rs10783292	0.83[ASN][1000 genomes]
rs10783293	0.88[ASN][1000 genomes]
rs10783294	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783295	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783297	0.94[ASN][1000 genomes]
rs10875886	0.87[ASN][1000 genomes]
rs10875893	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875894	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875895	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875896	0.84[ASN][1000 genomes]
rs10875897	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875898	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875899	0.82[ASN][1000 genomes]
rs10875900	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875901	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875902	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1111662	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11168779	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168783	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168784	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168785	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168790	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168792	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168794	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168795	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168797	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168798	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168800	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168801	0.90[ASN][1000 genomes]
rs11168803	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168811	0.84[ASN][1000 genomes]
rs11168812	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11608916	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11610459	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11610497	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11614474	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12227240	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12228521	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12229275	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12423542	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579249	0.88[ASN][1000 genomes]
rs1318692	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1690182	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1818996	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830192	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2030900	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070940	0.95[ASN][1000 genomes]
rs2073480	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2131713	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272311	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272312	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293449	0.88[ASN][1000 genomes]
rs2368701	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2453063	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2463175	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2694839	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2694840	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741627	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759146	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3782353	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809147	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825182	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3825184	0.86[ASN][1000 genomes]
rs4018510	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237854	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4433614	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4526804	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760600	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760661	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760662	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760663	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760664	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760665	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760666	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760667	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760668	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58023472	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59087236	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61941142	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61942166	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61942167	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61942169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61942207	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61942209	0.85[ASN][1000 genomes]
rs6580696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297958	0.88[ASN][1000 genomes]
rs7298330	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304942	0.88[ASN][1000 genomes]
rs7313988	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7489036	0.82[ASN][1000 genomes]
rs7963018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963160	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976473	0.90[ASN][1000 genomes]
rs833820	0.94[ASN][1000 genomes]
rs833821	0.94[ASN][1000 genomes]
rs833822	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs833827	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs833828	0.94[ASN][1000 genomes]
rs833839	0.86[ASN][1000 genomes]
rs833840	0.86[ASN][1000 genomes]
rs833841	0.86[ASN][1000 genomes]
rs833842	0.86[ASN][1000 genomes]
rs833843	0.83[ASN][1000 genomes]
rs961320	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9645813	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9783452	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9783477	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788029	0.89[ASN][1000 genomes]
rs9795742	0.86[ASN][1000 genomes]
rs9796008	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv899067	chr12:49329695-49344508	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2641450	RP11-302B13.1	cis	Whole Blood	GTEx
rs2641450	CCDC65	cis	Thyroid	GTEx
rs2641450	CCDC65	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49319800-49349400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:49329400-49349400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr12:49330600-49341400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:49330800-49349000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:49332000-49349000	Weak transcription	Stomach Mucosa	stomach
7	chr12:49333800-49349400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:49334200-49346200	Weak transcription	Fetal Kidney	kidney
9	chr12:49334600-49342200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:49334800-49342600	Weak transcription	K562	blood
11	chr12:49334800-49343600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:49334800-49346000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr12:49334800-49346400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:49334800-49348000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:49334800-49348600	Weak transcription	Small Intestine	intestine
16	chr12:49334800-49349400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:49334800-49349800	Weak transcription	Psoas Muscle	Psoas
18	chr12:49335000-49342200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:49335000-49346200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:49335000-49346600	Weak transcription	Ovary	ovary
21	chr12:49335000-49349400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:49335000-49349800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49335200-49346000	Weak transcription	NH-A	brain
24	chr12:49335200-49346200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:49335200-49346200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:49335200-49346400	Weak transcription	Aorta	Aorta
27	chr12:49335200-49349600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:49335400-49345800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:49335400-49349000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:49335400-49349400	Weak transcription	Liver	Liver
31	chr12:49335400-49349800	Weak transcription	Spleen	Spleen
32	chr12:49335800-49341400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:49335800-49345200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:49335800-49346200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:49335800-49346200	Weak transcription	NHLF	lung
36	chr12:49336000-49345800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:49336000-49346200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:49336000-49346200	Weak transcription	NHDF-Ad	bronchial
39	chr12:49336200-49343400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:49336600-49342600	Weak transcription	Fetal Thymus	thymus
41	chr12:49336600-49346200	Weak transcription	Osteobl	bone
42	chr12:49336600-49346400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:49337200-49346200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:49337400-49345800	Weak transcription	Thymus	Thymus
45	chr12:49337600-49345800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:49337600-49346000	Weak transcription	Placenta	Placenta
47	chr12:49337600-49346400	Weak transcription	Esophagus	oesophagus
48	chr12:49337600-49347800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:49337600-49349200	Weak transcription	Brain Substantia Nigra	brain
50	chr12:49337800-49341400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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