Variant report

Variant	rs11649624
Chromosome Location	chr16:70554101-70554102
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70549052..70551640-chr16:70553322..70555254,2	K562	blood:
2	chr16:70553189..70554990-chr16:70583388..70585891,2	MCF-7	breast:
3	chr16:70542244..70550034-chr16:70550058..70558887,15	MCF-7	breast:
4	chr16:70379094..70381917-chr16:70553437..70555581,2	K562	blood:

Variant related genes	Relation type
ENSG00000261777	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000168872	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10852465	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11075767	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11075768	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11075769	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075770	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11640374	0.84[EUR][1000 genomes]
rs11641683	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11643344	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11643373	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11643823	0.84[EUR][1000 genomes]
rs11645092	0.84[EUR][1000 genomes]
rs11645214	0.88[EUR][1000 genomes]
rs11645287	0.84[EUR][1000 genomes]
rs11645437	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11645585	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11648402	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11865527	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11866400	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12597401	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12909	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12925729	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12931402	0.82[EUR][1000 genomes]
rs12933634	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2168606	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288491	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303792	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2303793	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33910368	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34567847	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34890962	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762171	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4277334	0.81[EUR][1000 genomes]
rs4284632	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4324119	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4436771	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4513092	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4592653	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58963621	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499320	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499321	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71401814	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7194521	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7195030	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7197262	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7197840	0.88[EUR][1000 genomes]
rs7198317	0.87[EUR][1000 genomes]
rs7199859	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7200430	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7201750	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7204583	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722579	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8045651	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046881	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8049641	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8049786	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8051506	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8052031	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8052125	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8053436	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8057610	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8062178	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8063990	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8064013	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9635522	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9929904	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9936225	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11649624	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs11649624	EXOSC6	Cis_1M	lymphoblastoid	RTeQTL
rs11649624	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11649624	RP11-296I10.6	cis	Whole Blood	GTEx
rs11649624	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs11649624	CLEC18A	cis	Whole Blood	GTEx
rs11649624	RP11-296I10.6	cis	Muscle Skeletal	GTEx
rs11649624	RP11-296I10.6	cis	Thyroid	GTEx
rs11649624	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs11649624	RP11-296I10.6	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70489400-70556400	Weak transcription	Stomach Mucosa	stomach
2	chr16:70512800-70556400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70528800-70556400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:70541200-70556200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:70543000-70556200	Weak transcription	Fetal Heart	heart
6	chr16:70545000-70556200	Weak transcription	Small Intestine	intestine
7	chr16:70546200-70556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr16:70546400-70556400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr16:70546600-70556400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:70546800-70556400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr16:70547000-70554600	Weak transcription	HMEC	breast
12	chr16:70548400-70554400	Weak transcription	HUVEC	blood vessel
13	chr16:70548600-70554600	Weak transcription	NHEK	skin
14	chr16:70548800-70556000	Weak transcription	Psoas Muscle	Psoas
15	chr16:70548800-70556200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr16:70550000-70556200	Weak transcription	Fetal Brain Male	brain
17	chr16:70550200-70554400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:70550400-70556800	Weak transcription	Esophagus	oesophagus
19	chr16:70551200-70555000	Weak transcription	Right Ventricle	heart
20	chr16:70551200-70556800	Weak transcription	Aorta	Aorta
21	chr16:70551400-70554800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr16:70551400-70555000	Weak transcription	Lung	lung
23	chr16:70551400-70556200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:70551400-70556200	Weak transcription	Gastric	stomach
25	chr16:70551400-70556400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr16:70551600-70554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr16:70551600-70556000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:70551600-70556000	Weak transcription	Hela-S3	cervix
29	chr16:70551600-70556200	Weak transcription	Colonic Mucosa	Colon
30	chr16:70551600-70556400	Weak transcription	Colon Smooth Muscle	Colon
31	chr16:70551800-70554800	Weak transcription	NHLF	lung
32	chr16:70551800-70556400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr16:70552000-70554400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:70552000-70555000	Weak transcription	HepG2	liver
35	chr16:70552000-70556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr16:70552200-70554400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr16:70552200-70554800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:70552200-70555200	Weak transcription	Spleen	Spleen
39	chr16:70552200-70556200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr16:70552200-70556200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr16:70552200-70556200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr16:70552200-70556200	Weak transcription	A549	lung
43	chr16:70552200-70556400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr16:70552400-70554400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr16:70552400-70554400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr16:70552400-70554400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr16:70552400-70554400	Weak transcription	GM12878-XiMat	blood
48	chr16:70552400-70554600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr16:70552400-70554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr16:70552400-70554600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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