Variant report

Variant	rs2991978
Chromosome Location	chr1:46054486-46054487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46012797..46020877-chr1:46047985..46055272,23	K562	blood:
2	chr1:46052156..46055587-chr1:46081962..46085100,3	K562	blood:
3	chr1:46054087..46055930-chr1:46081362..46083462,2	K562	blood:
4	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
5	chr1:46048069..46054740-chr1:46150080..46155979,19	K562	blood:
6	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
7	chr1:46048586..46052942-chr1:46053282..46058031,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159596	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 177 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:169)

rs_ID	r²[population]
rs10430105	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10749856	0.83[EUR][1000 genomes]
rs10789467	0.86[EUR][1000 genomes]
rs10789468	0.84[EUR][1000 genomes]
rs10789470	0.85[EUR][1000 genomes]
rs10789471	0.81[EUR][1000 genomes]
rs1084086	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10890333	0.88[EUR][1000 genomes]
rs10890334	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890335	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890336	0.89[EUR][1000 genomes]
rs10890337	0.84[EUR][1000 genomes]
rs10890340	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10890341	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10890342	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10890343	0.84[EUR][1000 genomes]
rs10890344	0.83[EUR][1000 genomes]
rs10890345	0.81[EUR][1000 genomes]
rs11211142	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211145	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211146	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211147	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211149	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211151	0.89[EUR][1000 genomes]
rs11211152	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211157	0.85[EUR][1000 genomes]
rs11211158	0.84[EUR][1000 genomes]
rs11211159	0.84[EUR][1000 genomes]
rs11211160	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211161	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211162	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11211163	0.85[EUR][1000 genomes]
rs11211165	0.84[EUR][1000 genomes]
rs11211166	0.84[EUR][1000 genomes]
rs11211168	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211169	0.84[EUR][1000 genomes]
rs11211170	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211171	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211173	0.80[EUR][1000 genomes]
rs1135812	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1135850	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12022673	0.85[EUR][1000 genomes]
rs12023439	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024590	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025613	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12027622	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12037459	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12037803	0.85[EUR][1000 genomes]
rs12041197	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041677	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12043945	0.89[EUR][1000 genomes]
rs12045096	0.87[EUR][1000 genomes]
rs12045451	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047629	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12048866	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12049027	0.86[EUR][1000 genomes]
rs12062535	0.81[EUR][1000 genomes]
rs12070775	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12081175	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12091503	0.89[EUR][1000 genomes]
rs1250	0.92[EUR][1000 genomes]
rs1541131	0.95[EUR][1000 genomes]
rs1547924	0.95[EUR][1000 genomes]
rs1547925	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972410	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2050376	0.95[EUR][1000 genomes]
rs2152078	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230658	0.95[EUR][1000 genomes]
rs2230659	0.91[EUR][1000 genomes]
rs2253862	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2275085	0.94[EUR][1000 genomes]
rs2275086	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28361459	0.82[EUR][1000 genomes]
rs28370457	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28375469	0.83[EUR][1000 genomes]
rs28396194	0.81[EUR][1000 genomes]
rs28406914	0.82[EUR][1000 genomes]
rs28432365	0.82[EUR][1000 genomes]
rs28438704	0.82[EUR][1000 genomes]
rs28441217	0.82[EUR][1000 genomes]
rs28442079	0.82[EUR][1000 genomes]
rs28474773	0.82[EUR][1000 genomes]
rs28490344	0.81[EUR][1000 genomes]
rs28495425	0.82[EUR][1000 genomes]
rs28501477	0.81[EUR][1000 genomes]
rs28507722	0.82[EUR][1000 genomes]
rs28513660	0.82[EUR][1000 genomes]
rs28528139	0.82[EUR][1000 genomes]
rs28545085	0.82[EUR][1000 genomes]
rs28550303	0.83[EUR][1000 genomes]
rs28564319	0.82[EUR][1000 genomes]
rs28568986	0.82[EUR][1000 genomes]
rs28617418	0.80[EUR][1000 genomes]
rs28623463	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28719889	0.83[EUR][1000 genomes]
rs28752166	0.81[EUR][1000 genomes]
rs28789495	0.82[EUR][1000 genomes]
rs28812624	0.82[EUR][1000 genomes]
rs28817701	0.82[EUR][1000 genomes]
rs28862324	0.83[EUR][1000 genomes]
rs28890893	0.83[EUR][1000 genomes]
rs2991976	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2991977	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991979	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991980	0.81[AMR][1000 genomes]
rs2991981	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991983	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2991986	0.95[EUR][1000 genomes]
rs2991987	0.95[EUR][1000 genomes]
rs2991988	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2991989	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014210	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3014212	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3014213	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3014235	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3014236	0.93[EUR][1000 genomes]
rs3014237	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3014239	0.95[EUR][1000 genomes]
rs3014240	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3014245	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014246	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3014248	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3014249	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3014251	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3811435	0.84[EUR][1000 genomes]
rs3811436	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3935296	0.81[EUR][1000 genomes]
rs4415615	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4423054	0.81[EUR][1000 genomes]
rs4431884	0.89[EUR][1000 genomes]
rs4439382	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4559551	0.82[EUR][1000 genomes]
rs4564187	0.82[EUR][1000 genomes]
rs4586014	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4607935	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4609469	0.87[EUR][1000 genomes]
rs4660313	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660879	0.82[EUR][1000 genomes]
rs4660880	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499600	0.87[ASN][1000 genomes]
rs514595	0.87[ASN][1000 genomes]
rs563799	0.91[AMR][1000 genomes]
rs61062981	0.82[EUR][1000 genomes]
rs61784793	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61784795	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61784796	0.84[EUR][1000 genomes]
rs61784799	0.83[EUR][1000 genomes]
rs61784800	0.80[EUR][1000 genomes]
rs61784803	0.81[EUR][1000 genomes]
rs6429574	0.84[EUR][1000 genomes]
rs6429575	0.84[EUR][1000 genomes]
rs6658700	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6662164	0.80[EUR][1000 genomes]
rs6665808	0.85[EUR][1000 genomes]
rs66682726	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6686944	0.80[EUR][1000 genomes]
rs6690926	0.84[EUR][1000 genomes]
rs6694889	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6699418	0.88[EUR][1000 genomes]
rs6699444	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6703748	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7529699	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7545118	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7547414	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8179296	0.84[EUR][1000 genomes]
rs8179402	0.84[EUR][1000 genomes]
rs9429171	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429172	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9793568	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
3	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
4	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
5	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	esv3342998	chr1:46035908-46066462	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2991978	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs2991978	GPBP1L1	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46050800-46060200	Weak transcription	Aorta	Aorta
2	chr1:46051000-46055800	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:46051400-46069800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:46051600-46055000	Weak transcription	A549	lung
5	chr1:46051600-46055800	Weak transcription	Psoas Muscle	Psoas
6	chr1:46051600-46056200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:46051600-46060000	Weak transcription	HSMMtube	muscle
8	chr1:46051600-46060200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:46051800-46054800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:46051800-46055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:46051800-46060000	Weak transcription	Fetal Kidney	kidney
12	chr1:46052000-46056400	Weak transcription	Brain Substantia Nigra	brain
13	chr1:46052000-46057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:46052000-46081000	Weak transcription	Small Intestine	intestine
15	chr1:46052200-46054800	Weak transcription	Left Ventricle	heart
16	chr1:46052200-46055600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:46052200-46056800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:46052200-46057600	Weak transcription	Lung	lung
19	chr1:46052200-46058400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:46052200-46060000	Weak transcription	Esophagus	oesophagus
21	chr1:46052200-46063800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:46052200-46084200	Weak transcription	Right Atrium	heart
23	chr1:46052400-46055800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:46052400-46056400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:46052400-46056600	Weak transcription	HSMM	muscle
26	chr1:46052400-46057000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:46052400-46057000	Weak transcription	Fetal Stomach	stomach
28	chr1:46052400-46057800	Weak transcription	Brain Anterior Caudate	brain
29	chr1:46052400-46058400	Weak transcription	Fetal Lung	lung
30	chr1:46052400-46058400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:46052400-46059600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:46052400-46060200	Weak transcription	Colonic Mucosa	Colon
33	chr1:46052400-46060800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:46052400-46080600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:46052600-46055800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:46052600-46057000	Weak transcription	Fetal Intestine Large	intestine
37	chr1:46052600-46060200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:46052800-46054600	Weak transcription	Fetal Heart	heart
39	chr1:46052800-46054600	Genic enhancers	K562	blood
40	chr1:46052800-46054800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:46052800-46055000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:46052800-46055400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:46052800-46055400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:46052800-46055400	Weak transcription	Liver	Liver
45	chr1:46052800-46055400	Weak transcription	NH-A	brain
46	chr1:46052800-46055400	Weak transcription	NHEK	skin
47	chr1:46052800-46055600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:46052800-46055800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:46052800-46055800	Weak transcription	Right Ventricle	heart
50	chr1:46052800-46056000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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