Variant report

Variant	rs7789440
Chromosome Location	chr7:97888798-97888799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10808107	0.81[EUR][1000 genomes]
rs10953245	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953248	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10953255	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10953256	0.81[EUR][1000 genomes]
rs10953257	0.80[ASN][1000 genomes]
rs1132971	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11760930	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11761158	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11765794	0.80[ASN][1000 genomes]
rs11766808	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772293	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12667634	0.80[ASN][1000 genomes]
rs12673586	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12704977	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12704982	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12704983	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12873	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13232181	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13237878	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13238610	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13246725	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13246843	0.81[EUR][1000 genomes]
rs13246942	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1468338	0.81[EUR][1000 genomes]
rs17436977	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107716	0.85[EUR][1000 genomes]
rs2286074	0.81[EUR][1000 genomes]
rs2291747	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394852	0.85[EUR][1000 genomes]
rs34129434	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34304553	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34534766	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34695842	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34717219	0.80[ASN][1000 genomes]
rs34776142	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34789614	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34817002	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34830366	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34835415	0.80[ASN][1000 genomes]
rs35216698	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35527492	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35535338	0.80[ASN][1000 genomes]
rs35941058	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35944487	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35997266	0.80[ASN][1000 genomes]
rs36017146	0.80[ASN][1000 genomes]
rs36099592	0.81[EUR][1000 genomes]
rs3779194	0.81[EUR][1000 genomes]
rs3801254	0.81[EUR][1000 genomes]
rs3801255	0.81[EUR][1000 genomes]
rs3801263	0.80[ASN][1000 genomes]
rs3801264	0.81[EUR][1000 genomes]
rs3816944	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823740	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4075057	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56229643	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62479822	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62479823	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62479853	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6465661	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465662	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6465663	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6465664	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6465665	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6465666	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6465667	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465669	0.80[ASN][1000 genomes]
rs6465670	0.80[ASN][1000 genomes]
rs6465672	0.80[ASN][1000 genomes]
rs6465675	0.80[ASN][1000 genomes]
rs6465677	0.81[EUR][1000 genomes]
rs6465678	0.81[EUR][1000 genomes]
rs6465680	0.80[EUR][1000 genomes]
rs66548074	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6945554	0.80[ASN][1000 genomes]
rs6947208	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6947340	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6948346	0.80[ASN][1000 genomes]
rs6948540	0.80[ASN][1000 genomes]
rs6949214	0.80[ASN][1000 genomes]
rs6949718	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6950994	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955259	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6955647	0.81[EUR][1000 genomes]
rs6956686	0.81[EUR][1000 genomes]
rs6961129	0.80[ASN][1000 genomes]
rs6961438	0.81[EUR][1000 genomes]
rs6961790	0.81[EUR][1000 genomes]
rs6963210	0.81[EUR][1000 genomes]
rs6967457	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6967934	0.80[ASN][1000 genomes]
rs6968144	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6968193	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6968321	0.80[ASN][1000 genomes]
rs6969731	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6970801	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6970990	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6971825	0.80[ASN][1000 genomes]
rs6973775	0.81[EUR][1000 genomes]
rs6974943	0.80[ASN][1000 genomes]
rs6975156	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6979373	0.80[ASN][1000 genomes]
rs73147342	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73151177	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs736753	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs736754	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7458551	0.81[EUR][1000 genomes]
rs747633	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776638	0.81[EUR][1000 genomes]
rs7777415	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7781916	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7785612	0.83[EUR][1000 genomes]
rs7787858	0.81[EUR][1000 genomes]
rs7789380	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7790229	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7791321	0.85[EUR][1000 genomes]
rs7794187	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794612	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7795176	0.80[ASN][1000 genomes]
rs7796611	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7796762	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7797943	0.81[EUR][1000 genomes]
rs7801992	0.80[ASN][1000 genomes]
rs7802382	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7802541	0.83[EUR][1000 genomes]
rs7802560	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7802794	0.87[EUR][1000 genomes]
rs7806739	0.80[EUR][1000 genomes]
rs7807455	0.82[ASN][1000 genomes]
rs7807555	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9648908	0.80[EUR][1000 genomes]
rs9769767	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7789440	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs7789440	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97882200-97889400	Weak transcription	Small Intestine	intestine
2	chr7:97882200-97893200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:97882400-97890800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:97882400-97894400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:97882400-97895200	Weak transcription	NHDF-Ad	bronchial
6	chr7:97882400-97895400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:97882600-97889000	Weak transcription	Colon Smooth Muscle	Colon
8	chr7:97882600-97890000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:97882600-97890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:97882600-97892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:97882600-97892800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:97882600-97893000	Weak transcription	Brain Germinal Matrix	brain
13	chr7:97882800-97890000	Weak transcription	HSMMtube	muscle
14	chr7:97882800-97895000	Weak transcription	HUVEC	blood vessel
15	chr7:97882800-97895200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:97882800-97895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:97882800-97895200	Weak transcription	NH-A	brain
18	chr7:97882800-97895200	Weak transcription	NHLF	lung
19	chr7:97883000-97890000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:97883000-97890000	Weak transcription	GM12878-XiMat	blood
21	chr7:97883000-97890200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:97883000-97890200	Weak transcription	Brain Hippocampus Middle	brain
23	chr7:97883000-97890200	Weak transcription	Hela-S3	cervix
24	chr7:97883000-97890800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:97883000-97890800	Weak transcription	A549	lung
26	chr7:97883000-97893000	Weak transcription	Stomach Mucosa	stomach
27	chr7:97883000-97893400	Weak transcription	Colonic Mucosa	Colon
28	chr7:97883000-97894800	Weak transcription	Fetal Brain Male	brain
29	chr7:97883600-97890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:97884600-97891000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:97884600-97894400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:97885600-97891400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:97886000-97890200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:97886000-97891600	Strong transcription	Fetal Intestine Small	intestine
35	chr7:97886600-97890000	Weak transcription	Fetal Intestine Large	intestine
36	chr7:97886600-97890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:97886600-97890600	Weak transcription	Aorta	Aorta
38	chr7:97886600-97890600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:97886600-97895200	Weak transcription	HepG2	liver
40	chr7:97886600-97896600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:97886600-97909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr7:97886800-97890000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:97886800-97890200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:97886800-97890600	Weak transcription	Dnd41	blood
45	chr7:97886800-97890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:97886800-97909200	Weak transcription	Brain Substantia Nigra	brain
47	chr7:97886800-97910000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:97887200-97888800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr7:97887200-97889800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:97887200-97890000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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