Variant report

Variant	rs12539676
Chromosome Location	chr7:97888478-97888479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10249366	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10953247	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11761574	0.90[EUR][1000 genomes]
rs11771397	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11771953	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11772438	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11773779	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11984183	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12533016	0.88[EUR][1000 genomes]
rs12669622	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12704981	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270600	0.89[EUR][1000 genomes]
rs2270604	0.88[EUR][1000 genomes]
rs2394827	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28566958	0.88[EUR][1000 genomes]
rs28662014	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4727388	0.90[EUR][1000 genomes]
rs4727390	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4729421	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56098787	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61575270	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62479836	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62479838	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6951479	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747631	0.89[EUR][1000 genomes]
rs747632	0.89[EUR][1000 genomes]
rs7787309	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs954050	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][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
rs12539676	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL
rs12539676	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 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	chr7:97882400-97888600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:97882400-97888600	Weak transcription	Fetal Lung	lung
5	chr7:97882400-97890800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:97882400-97894400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:97882400-97895200	Weak transcription	NHDF-Ad	bronchial
8	chr7:97882400-97895400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:97882600-97888600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:97882600-97889000	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:97882600-97890000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:97882600-97890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:97882600-97892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:97882600-97892800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:97882600-97893000	Weak transcription	Brain Germinal Matrix	brain
16	chr7:97882800-97890000	Weak transcription	HSMMtube	muscle
17	chr7:97882800-97895000	Weak transcription	HUVEC	blood vessel
18	chr7:97882800-97895200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:97882800-97895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:97882800-97895200	Weak transcription	NH-A	brain
21	chr7:97882800-97895200	Weak transcription	NHLF	lung
22	chr7:97883000-97890000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:97883000-97890000	Weak transcription	GM12878-XiMat	blood
24	chr7:97883000-97890200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr7:97883000-97890200	Weak transcription	Brain Hippocampus Middle	brain
26	chr7:97883000-97890200	Weak transcription	Hela-S3	cervix
27	chr7:97883000-97890800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:97883000-97890800	Weak transcription	A549	lung
29	chr7:97883000-97893000	Weak transcription	Stomach Mucosa	stomach
30	chr7:97883000-97893400	Weak transcription	Colonic Mucosa	Colon
31	chr7:97883000-97894800	Weak transcription	Fetal Brain Male	brain
32	chr7:97883600-97890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:97884600-97891000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr7:97884600-97894400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr7:97884800-97888600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:97885600-97891400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:97886000-97890200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:97886000-97891600	Strong transcription	Fetal Intestine Small	intestine
39	chr7:97886600-97890000	Weak transcription	Fetal Intestine Large	intestine
40	chr7:97886600-97890200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:97886600-97890600	Weak transcription	Aorta	Aorta
42	chr7:97886600-97890600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr7:97886600-97895200	Weak transcription	HepG2	liver
44	chr7:97886600-97896600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:97886600-97909800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr7:97886800-97890000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr7:97886800-97890200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:97886800-97890600	Weak transcription	Dnd41	blood
49	chr7:97886800-97890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:97886800-97909200	Weak transcription	Brain Substantia Nigra	brain

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