Variant report

Variant	rs12531365
Chromosome Location	chr7:66259954-66259955
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	GATA3	chr7:66259865-66260026	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66258319..66260099-chr7:66263476..66266202,2	K562	blood:
2	chr7:66258312..66261125-chr7:66262696..66264918,2	K562	blood:

Variant related genes	Relation type
RABGEF1	TF binding region
ENSG00000238841	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10232188	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10235334	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10235423	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10236124	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10237309	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10247591	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10250831	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10264223	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264873	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10267922	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10269487	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10270138	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10275343	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275956	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279240	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10281794	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10479729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532805	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532829	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12533298	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12533724	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534188	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12534948	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12536003	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12537176	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12537474	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12538038	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540371	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1589887	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17138017	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17680606	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1984651	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2077180	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091315	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28510688	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28524571	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28590087	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28729561	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778914	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3778916	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4382352	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4617036	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4717326	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56743740	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59765110	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61554495	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62465677	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62465679	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62465704	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62465717	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62465731	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62465735	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62465746	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465749	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62465751	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62465753	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62466579	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62466580	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73140000	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73143914	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7785755	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr7:66236800-66276800	Strong transcription	Dnd41	blood
6	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
9	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr7:66240400-66260000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:66242200-66260000	Weak transcription	Psoas Muscle	Psoas
13	chr7:66242400-66262600	Weak transcription	Colonic Mucosa	Colon
14	chr7:66243600-66263200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:66245600-66279200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:66245600-66279400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:66245800-66260400	Weak transcription	HUVEC	blood vessel
18	chr7:66246200-66277800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr7:66246200-66279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:66246800-66261400	Weak transcription	Esophagus	oesophagus
21	chr7:66247000-66260800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr7:66247600-66261000	Weak transcription	Brain Substantia Nigra	brain
23	chr7:66248400-66277800	Strong transcription	Osteobl	bone
24	chr7:66248600-66276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:66248800-66277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr7:66249400-66278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:66250000-66279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr7:66250000-66279200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:66250200-66277800	Strong transcription	Primary T cells from cord blood	blood
30	chr7:66250200-66278600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr7:66253200-66277600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:66254000-66277400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:66254000-66278400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:66254200-66276000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:66254200-66277200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:66254200-66278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:66254600-66278600	Strong transcription	HSMM	muscle
38	chr7:66254800-66263000	Strong transcription	NH-A	brain
39	chr7:66254800-66267400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:66254800-66268600	Strong transcription	GM12878-XiMat	blood
41	chr7:66254800-66275800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:66254800-66276200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr7:66254800-66276800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr7:66254800-66276800	Strong transcription	HepG2	liver
45	chr7:66254800-66277800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr7:66255000-66262000	Weak transcription	Right Ventricle	heart
47	chr7:66255000-66264600	Strong transcription	Primary B cells from cord blood	blood
48	chr7:66255200-66267400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr7:66255200-66268600	Strong transcription	Brain Anterior Caudate	brain
50	chr7:66255200-66277000	Strong transcription	HMEC	breast

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