Variant report

Variant	rs3779494
Chromosome Location	chr7:107250355-107250356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107249922..107251734-chr7:107254251..107256132,2	K562	blood:
2	chr7:107246999..107250593-chr7:107255089..107256858,3	MCF-7	breast:
3	chr7:107243079..107246883-chr7:107249270..107252671,3	K562	blood:
4	chr7:107249634..107253526-chr7:107253696..107258280,6	K562	blood:

Variant related genes	Relation type
ENSG00000238832	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1015411	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10234355	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10237948	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243340	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10251808	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10258385	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10264412	0.87[ASN][1000 genomes]
rs10267907	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10273733	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10274041	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10276604	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10281535	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11535285	0.82[ASN][1000 genomes]
rs11771278	0.83[EUR][1000 genomes]
rs11977187	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12667527	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12668402	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673675	0.84[EUR][1000 genomes]
rs13228252	0.82[EUR][1000 genomes]
rs1468336	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1544336	0.84[EUR][1000 genomes]
rs17154077	0.84[EUR][1000 genomes]
rs17154091	0.80[ASN][1000 genomes]
rs17154104	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2023685	0.85[ASN][1000 genomes]
rs2057837	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066735	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107713	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2178497	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2189839	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237670	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237671	0.81[ASN][1000 genomes]
rs2237672	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237673	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2237676	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237677	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237678	0.87[ASN][1000 genomes]
rs2250414	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2253146	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253269	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253271	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253833	0.87[ASN][1000 genomes]
rs2293658	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395882	0.80[ASN][1000 genomes]
rs2395883	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395907	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2520241	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520242	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520243	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520245	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520246	0.82[ASN][1000 genomes]
rs2520247	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2520249	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2520250	0.81[ASN][1000 genomes]
rs2520252	0.82[ASN][1000 genomes]
rs2520256	0.84[ASN][1000 genomes]
rs2520260	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520261	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520263	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520264	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520265	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520267	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2520268	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2520269	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2520271	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2520277	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712189	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2712191	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2712193	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712195	0.82[ASN][1000 genomes]
rs2712196	0.82[ASN][1000 genomes]
rs2712197	0.81[ASN][1000 genomes]
rs2712199	0.81[ASN][1000 genomes]
rs2712200	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2712201	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2712214	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712215	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712224	0.86[ASN][1000 genomes]
rs2712228	0.84[EUR][1000 genomes]
rs2712229	0.91[EUR][1000 genomes]
rs2807	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2808	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28687365	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28714607	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2894466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2894475	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3094383	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34325395	0.82[ASN][1000 genomes]
rs3779495	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3801944	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801948	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801954	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4727679	0.80[ASN][1000 genomes]
rs4727680	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4727681	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4727684	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4730245	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56967324	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57452492	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58052742	0.87[ASN][1000 genomes]
rs62482543	0.83[EUR][1000 genomes]
rs62483722	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483723	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483725	0.87[ASN][1000 genomes]
rs62483727	0.89[ASN][1000 genomes]
rs67982599	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6976607	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7778250	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7778270	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7782057	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7786801	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7790534	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7793613	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7803102	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7806835	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7809950	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs986994	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs987391	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv608074	chr7:107179131-107260856	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3779494	BCAP29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107221200-107272000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:107221400-107253800	Weak transcription	Ovary	ovary
3	chr7:107221400-107254200	Weak transcription	Thymus	Thymus
4	chr7:107221400-107256400	Weak transcription	Lung	lung
5	chr7:107221400-107272400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:107221400-107276000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:107221600-107254200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:107222400-107258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:107223000-107254400	Weak transcription	Brain Germinal Matrix	brain
10	chr7:107223400-107256800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:107223600-107254400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:107223600-107256600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:107225600-107254000	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:107226200-107254000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:107226800-107254200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:107226800-107254800	Weak transcription	Fetal Thymus	thymus
17	chr7:107227800-107253800	Weak transcription	Brain Angular Gyrus	brain
18	chr7:107227800-107265400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:107230200-107256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:107233600-107256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:107235200-107271800	Weak transcription	Small Intestine	intestine
22	chr7:107235800-107254000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:107235800-107254400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:107235800-107268200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:107236000-107254400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr7:107236000-107254600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:107236000-107262800	Weak transcription	GM12878-XiMat	blood
28	chr7:107236000-107270800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:107236400-107255000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:107236400-107256600	Weak transcription	A549	lung
31	chr7:107236600-107254000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:107237200-107254400	Weak transcription	NHLF	lung
33	chr7:107237600-107250400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:107237600-107252600	Weak transcription	Fetal Intestine Small	intestine
35	chr7:107237800-107254200	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:107237800-107254400	Weak transcription	Pancreas	Pancrea
37	chr7:107238000-107254000	Weak transcription	HSMMtube	muscle
38	chr7:107238000-107254400	Weak transcription	Psoas Muscle	Psoas
39	chr7:107238000-107272000	Weak transcription	Esophagus	oesophagus
40	chr7:107238600-107254400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:107238800-107253000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr7:107238800-107253600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:107239200-107253800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr7:107239200-107254400	Weak transcription	Hela-S3	cervix
45	chr7:107240800-107254600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:107241200-107253800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:107241800-107254000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:107241800-107254000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr7:107241800-107254000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:107241800-107254200	Weak transcription	Brain Substantia Nigra	brain

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