Variant report

Variant	rs62466451
Chromosome Location	chr7:66811955-66811956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66806712..66809740-chr7:66809964..66812550,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11971862	0.86[ASN][1000 genomes]
rs11976226	0.86[ASN][1000 genomes]
rs12530552	0.86[ASN][1000 genomes]
rs12530786	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12531602	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12532084	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12532409	0.82[ASN][1000 genomes]
rs12532437	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532798	0.86[ASN][1000 genomes]
rs12532952	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12534196	0.86[ASN][1000 genomes]
rs12534273	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534602	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12534872	0.84[EUR][1000 genomes]
rs12535489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535529	0.83[ASN][1000 genomes]
rs12535715	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12537527	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537772	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17140742	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17144955	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17145211	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17786435	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277021	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34737375	0.84[ASN][1000 genomes]
rs41533347	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717368	0.82[EUR][1000 genomes]
rs4717374	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4717380	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717382	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4718526	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718552	0.89[ASN][1000 genomes]
rs4718558	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56878889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57571548	1.00[AFR][1000 genomes]
rs58757717	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60593769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61657086	1.00[ASN][1000 genomes]
rs62466395	0.81[AMR][1000 genomes]
rs62466401	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466404	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62466433	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62466442	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62466449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62466450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467568	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62467573	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467574	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467575	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62467578	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62467579	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73124053	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1027702	chr7:66722103-66841913	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031048	chr7:66722103-66844039	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv966839	chr7:66805198-66815088	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1031560	chr7:66805244-66846663	Enhancers Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022779	chr7:66805244-66849392	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv970413	chr7:66808251-66815088	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1031147	chr7:66811313-66922350	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62466451	FLJ13195	Cis_1M	lymphoblastoid	RTeQTL
rs62466451	STAG3L4	cis	Artery Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66785800-66816200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:66801200-66812000	Weak transcription	Gastric	stomach
3	chr7:66802800-66814800	Weak transcription	HSMMtube	muscle
4	chr7:66805200-66816200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr7:66806200-66813400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:66807200-66819600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:66807200-66822400	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:66808400-66816200	Weak transcription	Thymus	Thymus
9	chr7:66808400-66822200	Weak transcription	Right Ventricle	heart
10	chr7:66808800-66815600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:66809000-66812400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
12	chr7:66809200-66812400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:66809200-66813000	Weak transcription	Brain Germinal Matrix	brain
14	chr7:66809800-66812400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:66809800-66815000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr7:66809800-66816000	Weak transcription	Dnd41	blood
17	chr7:66809800-66822600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:66809800-66822800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:66810000-66816400	Weak transcription	Colon Smooth Muscle	Colon
20	chr7:66810000-66820800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:66810000-66822200	Weak transcription	Aorta	Aorta
22	chr7:66810000-66822200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:66810200-66812000	Weak transcription	Fetal Intestine Large	intestine
24	chr7:66810200-66812800	Weak transcription	Primary B cells from cord blood	blood
25	chr7:66810200-66813000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:66810200-66816800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:66810200-66821400	Weak transcription	Ovary	ovary
28	chr7:66810200-66821600	Weak transcription	Adipose Nuclei	Adipose
29	chr7:66810200-66821800	Weak transcription	Liver	Liver
30	chr7:66810200-66822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:66810200-66822200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:66810200-66822800	Weak transcription	Brain Angular Gyrus	brain
33	chr7:66810200-66830400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:66810400-66812800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr7:66810400-66813600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:66810400-66815000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:66810400-66815800	Weak transcription	Placenta	Placenta
38	chr7:66810400-66819800	Weak transcription	Primary T cells from cord blood	blood
39	chr7:66810600-66813600	Strong transcription	Fetal Stomach	stomach
40	chr7:66810600-66821000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:66811000-66812200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr7:66811200-66818000	Weak transcription	Left Ventricle	heart
43	chr7:66811200-66822000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:66811200-66822000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:66811400-66812200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr7:66811600-66822800	Weak transcription	Brain Substantia Nigra	brain
47	chr7:66811600-66826000	Weak transcription	Psoas Muscle	Psoas
48	chr7:66811800-66812000	Active TSS	Stomach Mucosa	stomach

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