Variant report

Variant	rs7802541
Chromosome Location	chr7:97933855-97933856
allele	A/C
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	POLR2A	chr7:97933575-97933858	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:97933291..97935176-chr7:97935657..97937942,2	K562	blood:
2	chr7:97922907..97924787-chr7:97933166..97935079,2	K562	blood:
3	chr7:97922244..97926850-chr7:97930553..97934195,4	MCF-7	breast:

Variant related genes	Relation type
BRI3	TF binding region
ENSG00000272782	TF binding region
ENSG00000272782	Chromatin interaction
ENSG00000006453	Chromatin interaction
ENSG00000164713	Chromatin interaction

Extended variants
information (count: 180 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1076272	0.80[EUR][1000 genomes]
rs10808107	0.88[EUR][1000 genomes]
rs10953255	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10953256	0.88[EUR][1000 genomes]
rs10953257	0.87[EUR][1000 genomes]
rs1132971	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11760930	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11761158	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11761206	0.85[EUR][1000 genomes]
rs11765794	0.86[EUR][1000 genomes]
rs11766808	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11772293	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12112351	0.85[EUR][1000 genomes]
rs12667634	0.87[EUR][1000 genomes]
rs12672092	0.87[EUR][1000 genomes]
rs12673586	0.92[EUR][1000 genomes]
rs12704977	0.82[EUR][1000 genomes]
rs12704982	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12704983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12704988	0.86[EUR][1000 genomes]
rs12704989	0.81[EUR][1000 genomes]
rs12728	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12873	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13232181	0.93[EUR][1000 genomes]
rs13237102	0.83[EUR][1000 genomes]
rs13237878	0.82[EUR][1000 genomes]
rs13238610	0.89[EUR][1000 genomes]
rs13245076	0.85[EUR][1000 genomes]
rs13246725	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13246843	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13246868	0.87[EUR][1000 genomes]
rs13246942	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13307593	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1468338	0.88[EUR][1000 genomes]
rs1468340	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1468341	0.87[EUR][1000 genomes]
rs17436977	0.81[EUR][1000 genomes]
rs1859482	0.86[EUR][1000 genomes]
rs2107716	0.92[EUR][1000 genomes]
rs2158553	0.87[EUR][1000 genomes]
rs2240349	0.87[EUR][1000 genomes]
rs2286074	0.88[EUR][1000 genomes]
rs2394852	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2394854	0.83[EUR][1000 genomes]
rs34129434	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34534766	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34695842	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34717219	0.87[EUR][1000 genomes]
rs34776142	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34789614	0.81[EUR][1000 genomes]
rs34817002	0.82[EUR][1000 genomes]
rs34830366	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34835415	0.87[EUR][1000 genomes]
rs35216698	0.86[EUR][1000 genomes]
rs35535338	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35941058	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35944487	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35997266	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs36017146	0.87[EUR][1000 genomes]
rs36099592	0.88[EUR][1000 genomes]
rs3779193	0.82[EUR][1000 genomes]
rs3779194	0.88[EUR][1000 genomes]
rs3801251	0.82[EUR][1000 genomes]
rs3801254	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3801255	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3801256	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3801257	0.86[EUR][1000 genomes]
rs3801263	0.87[EUR][1000 genomes]
rs3801264	0.88[EUR][1000 genomes]
rs3816944	0.81[EUR][1000 genomes]
rs3823740	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4075057	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55825602	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs56286037	0.85[EUR][1000 genomes]
rs60077733	0.84[EUR][1000 genomes]
rs62478174	0.82[EUR][1000 genomes]
rs62478175	0.84[EUR][1000 genomes]
rs62478200	0.87[EUR][1000 genomes]
rs62478203	0.85[EUR][1000 genomes]
rs62478233	0.82[EUR][1000 genomes]
rs62479853	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6465661	0.81[EUR][1000 genomes]
rs6465662	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6465663	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465664	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6465665	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6465666	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6465667	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6465669	0.83[EUR][1000 genomes]
rs6465670	0.83[EUR][1000 genomes]
rs6465671	0.86[EUR][1000 genomes]
rs6465672	0.87[EUR][1000 genomes]
rs6465673	0.84[EUR][1000 genomes]
rs6465675	0.87[EUR][1000 genomes]
rs6465677	0.88[EUR][1000 genomes]
rs6465678	0.88[EUR][1000 genomes]
rs6465680	0.87[EUR][1000 genomes]
rs6465681	0.85[EUR][1000 genomes]
rs6465682	0.86[EUR][1000 genomes]
rs6465683	0.83[EUR][1000 genomes]
rs66548074	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67132564	0.87[EUR][1000 genomes]
rs6944262	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6945554	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6947208	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6947340	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6948346	0.83[EUR][1000 genomes]
rs6948540	0.86[EUR][1000 genomes]
rs6949214	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6949718	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6950994	0.82[EUR][1000 genomes]
rs6955259	0.84[EUR][1000 genomes]
rs6955647	0.88[EUR][1000 genomes]
rs6956686	0.88[EUR][1000 genomes]
rs6959506	0.87[EUR][1000 genomes]
rs6961129	0.87[EUR][1000 genomes]
rs6961438	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6961790	0.88[EUR][1000 genomes]
rs6963210	0.88[EUR][1000 genomes]
rs6967457	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6967576	0.86[EUR][1000 genomes]
rs6967934	0.83[EUR][1000 genomes]
rs6968144	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6968193	0.90[EUR][1000 genomes]
rs6968321	0.87[EUR][1000 genomes]
rs6969234	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6969731	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6970801	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6970990	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6971825	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6973775	0.88[EUR][1000 genomes]
rs6974943	0.87[EUR][1000 genomes]
rs6975156	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6979373	0.87[EUR][1000 genomes]
rs71563562	0.85[EUR][1000 genomes]
rs73147342	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs736753	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs736754	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7458551	0.88[EUR][1000 genomes]
rs7776638	0.88[EUR][1000 genomes]
rs7777415	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7781916	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7785612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7787418	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7787858	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7789380	0.88[EUR][1000 genomes]
rs7789440	0.83[EUR][1000 genomes]
rs7790229	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7791321	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7794187	0.84[EUR][1000 genomes]
rs7794612	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7795176	0.87[EUR][1000 genomes]
rs7796611	0.90[EUR][1000 genomes]
rs7796762	0.82[EUR][1000 genomes]
rs7797943	0.88[EUR][1000 genomes]
rs7801992	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7802382	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7802560	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7802794	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7803372	0.86[EUR][1000 genomes]
rs7805267	0.85[EUR][1000 genomes]
rs7806739	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7807455	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7807555	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7812180	0.85[EUR][1000 genomes]
rs9648908	0.87[EUR][1000 genomes]
rs9769767	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
9	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
10	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
11	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
12	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
13	nsv1016826	chr7:97926133-97963717	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7802541	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs7802541	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97914200-97958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:97919000-97941200	Weak transcription	Psoas Muscle	Psoas
3	chr7:97919200-97957600	Weak transcription	Right Atrium	heart
4	chr7:97922200-97935200	Weak transcription	Fetal Heart	heart
5	chr7:97922200-97946800	Weak transcription	Small Intestine	intestine
6	chr7:97922800-97935400	Weak transcription	Fetal Lung	lung
7	chr7:97923000-97935800	Weak transcription	GM12878-XiMat	blood
8	chr7:97923000-97942600	Weak transcription	Primary B cells from cord blood	blood
9	chr7:97923400-97936600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:97923400-97952000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:97923800-97936800	Weak transcription	Brain Anterior Caudate	brain
12	chr7:97924000-97937600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:97924200-97935800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:97924400-97935400	Weak transcription	Ovary	ovary
15	chr7:97924600-97952200	Weak transcription	Fetal Kidney	kidney
16	chr7:97924600-97952800	Weak transcription	NH-A	brain
17	chr7:97924800-97935600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:97924800-97942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:97925000-97935400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr7:97925000-97936800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:97925000-97937400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:97925000-97939000	Weak transcription	Brain Angular Gyrus	brain
23	chr7:97925200-97935400	Weak transcription	Left Ventricle	heart
24	chr7:97925200-97935600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:97925200-97941600	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:97926200-97936000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr7:97926600-97935800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr7:97926600-97942600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr7:97926800-97935600	Weak transcription	Osteobl	bone
30	chr7:97926800-97937600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:97927000-97942600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:97927200-97935800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:97927200-97939200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:97927600-97940400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:97927600-97948200	Weak transcription	Brain Germinal Matrix	brain
36	chr7:97928200-97939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr7:97928800-97947400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr7:97929000-97934200	Strong transcription	NHEK	skin
39	chr7:97929200-97937200	Strong transcription	Pancreas	Pancrea
40	chr7:97929400-97934000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:97929400-97934200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr7:97929400-97938000	Strong transcription	A549	lung
43	chr7:97929400-97939600	Strong transcription	Lung	lung
44	chr7:97929400-97942000	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:97929400-97945200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr7:97929400-97945800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr7:97929400-97947400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr7:97930400-97935200	Weak transcription	Stomach Mucosa	stomach
49	chr7:97930400-97936200	Strong transcription	HMEC	breast
50	chr7:97930400-97937000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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