Variant report

Variant	rs62466588
Chromosome Location	chr7:66458903-66458904
allele	C/T
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	NFIC	chr7:66458739-66459218	GM12878	blood:	n/a	n/a
2	RUNX3	chr7:66458731-66459185	GM12878	blood:	n/a	n/a
3	MEF2A	chr7:66458819-66459155	GM12878	blood:	n/a	chr7:66458945-66458966 chr7:66458945-66458966 chr7:66459056-66459067

No.	Distal block	Cell Line	Cell type
1	chr7:66458248..66462145-chr7:72299146..72302148,5	K562	blood:
2	chr7:66458802..66462145-chr7:72298376..72302148,5	K562	blood:
3	chr7:66426423..66428356-chr7:66456046..66459032,2	K562	blood:
4	chr7:66309584..66311542-chr7:66458819..66461691,3	K562	blood:

Variant related genes	Relation type
TYW1	TF binding region
ENSG00000225648	Chromatin interaction
ENSG00000230583	Chromatin interaction
ENSG00000254184	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs12531516	1.00[AMR][1000 genomes]
rs12532160	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12532307	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12532650	0.81[AMR][1000 genomes]
rs12533830	0.87[AMR][1000 genomes]
rs12534278	0.87[AMR][1000 genomes]
rs12534401	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12535023	0.87[AMR][1000 genomes]
rs12537353	0.87[AMR][1000 genomes]
rs12537414	0.87[AMR][1000 genomes]
rs12537825	0.93[AMR][1000 genomes]
rs12537955	0.87[AMR][1000 genomes]
rs12539366	0.87[AMR][1000 genomes]
rs12539604	0.81[AMR][1000 genomes]
rs12540695	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2091314	0.87[AMR][1000 genomes]
rs2293351	0.87[AMR][1000 genomes]
rs34758320	0.87[AMR][1000 genomes]
rs35448884	0.87[AMR][1000 genomes]
rs3800819	0.87[AMR][1000 genomes]
rs4717323	0.81[AMR][1000 genomes]
rs4717329	0.87[AMR][1000 genomes]
rs4717335	0.81[AMR][1000 genomes]
rs4718426	0.87[AMR][1000 genomes]
rs4718434	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4718438	0.81[AMR][1000 genomes]
rs4718450	0.87[AMR][1000 genomes]
rs62465700	0.81[AMR][1000 genomes]
rs62465701	0.81[AMR][1000 genomes]
rs62465705	0.81[AMR][1000 genomes]
rs62465734	0.87[AMR][1000 genomes]
rs62465736	0.87[AMR][1000 genomes]
rs62465738	0.87[AMR][1000 genomes]
rs62465739	0.87[AMR][1000 genomes]
rs62465740	0.87[AMR][1000 genomes]
rs62465741	0.87[AMR][1000 genomes]
rs62465742	0.87[AMR][1000 genomes]
rs62465743	0.87[AMR][1000 genomes]
rs62465744	0.87[AMR][1000 genomes]
rs62465745	0.87[AMR][1000 genomes]
rs62465747	0.87[AMR][1000 genomes]
rs62465748	0.87[AMR][1000 genomes]
rs62465750	0.87[AMR][1000 genomes]
rs62465752	0.87[AMR][1000 genomes]
rs62466575	0.87[AMR][1000 genomes]
rs62466582	1.00[AMR][1000 genomes]
rs62466584	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62466586	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62466589	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62466591	0.81[AMR][1000 genomes]
rs62466592	0.81[AMR][1000 genomes]
rs62466594	0.81[AMR][1000 genomes]
rs62466596	0.81[AMR][1000 genomes]
rs62466632	0.87[AMR][1000 genomes]
rs62466633	0.87[AMR][1000 genomes]
rs62466634	0.87[AMR][1000 genomes]
rs62466635	0.87[AMR][1000 genomes]
rs62466637	0.87[AMR][1000 genomes]
rs62466638	0.87[AMR][1000 genomes]
rs62466639	0.87[AMR][1000 genomes]
rs62466640	0.87[AMR][1000 genomes]
rs62466642	0.87[AMR][1000 genomes]
rs62466657	0.87[AMR][1000 genomes]
rs62466659	0.87[AMR][1000 genomes]
rs62468374	0.87[AMR][1000 genomes]
rs62468375	0.87[AMR][1000 genomes]
rs62468378	0.87[AMR][1000 genomes]
rs62468379	0.87[AMR][1000 genomes]
rs62468380	0.87[AMR][1000 genomes]
rs62468381	0.87[AMR][1000 genomes]
rs62468382	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62466588	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66420600-66459200	Weak transcription	Psoas Muscle	Psoas
2	chr7:66446600-66459400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:66449400-66459200	Weak transcription	HepG2	liver
4	chr7:66449600-66459400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:66451600-66459200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:66451600-66459400	Weak transcription	Esophagus	oesophagus
7	chr7:66451800-66459200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:66451800-66459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:66452000-66459200	Weak transcription	Aorta	Aorta
10	chr7:66452000-66459800	Weak transcription	Small Intestine	intestine
11	chr7:66452200-66459000	Weak transcription	Fetal Brain Male	brain
12	chr7:66452200-66459000	Weak transcription	Fetal Heart	heart
13	chr7:66452800-66459200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:66453600-66459000	Strong transcription	Fetal Intestine Small	intestine
15	chr7:66453600-66459600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:66454200-66459200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:66454200-66459400	Weak transcription	Gastric	stomach
18	chr7:66454200-66459600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:66454200-66460200	Weak transcription	Spleen	Spleen
20	chr7:66454400-66459400	Weak transcription	Lung	lung
21	chr7:66454400-66459600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:66455200-66459000	Strong transcription	K562	blood
23	chr7:66455200-66459000	Strong transcription	Osteobl	bone
24	chr7:66455400-66459800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:66455600-66459000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:66455800-66459000	Strong transcription	NHEK	skin
27	chr7:66456800-66459200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr7:66457000-66459600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr7:66457400-66459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:66457400-66459000	Weak transcription	A549	lung
31	chr7:66457400-66459200	Weak transcription	Primary B cells from cord blood	blood
32	chr7:66457400-66459200	Weak transcription	Fetal Brain Female	brain
33	chr7:66457400-66459400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:66457400-66459600	Weak transcription	Ovary	ovary
35	chr7:66457400-66459800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:66457600-66459200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:66457600-66459400	Weak transcription	Stomach Mucosa	stomach
38	chr7:66457800-66459000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:66457800-66459200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:66458000-66459200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:66458200-66459000	Genic enhancers	Brain Angular Gyrus	brain
42	chr7:66458200-66459200	Enhancers	Colonic Mucosa	Colon
43	chr7:66458400-66459000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr7:66458400-66459000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr7:66458400-66459000	Genic enhancers	Adipose Nuclei	Adipose
46	chr7:66458400-66459000	Genic enhancers	Dnd41	blood
47	chr7:66458400-66459000	Weak transcription	HSMM	muscle
48	chr7:66458400-66459200	Weak transcription	Brain Germinal Matrix	brain
49	chr7:66458400-66459200	Enhancers	Brain Hippocampus Middle	brain
50	chr7:66458400-66459200	Enhancers	Brain Substantia Nigra	brain

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