Variant report

Variant	rs12530898
Chromosome Location	chr7:65551384-65551385
allele	A/G
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	NR3C1	chr7:65551310-65551801	A549	lung:	n/a	n/a
2	NR3C1	chr7:65551270-65551877	A549	lung:	n/a	n/a
3	POLR2A	chr7:65550888-65551515	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:65551226-65551806	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:65550364..65553168-chr7:65578691..65580268,2	K562	blood:
2	chr7:65549975..65551527-chr7:65598587..65601084,2	K562	blood:
3	chr7:65550364..65554176-chr7:65578691..65580881,4	K562	blood:
4	chr7:65540457..65542538-chr7:65550059..65552910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249319	TF binding region
ASL	TF binding region
ENSG00000241258	Chromatin interaction
ENSG00000126522	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs12531358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12531900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12532327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532423	1.00[AFR][1000 genomes]
rs12532675	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12534109	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes]
rs12536292	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12537407	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12538147	1.00[AFR][1000 genomes]
rs12538379	1.00[AFR][1000 genomes]
rs12538961	1.00[AFR][1000 genomes]
rs12540888	1.00[AFR][1000 genomes]
rs2279904	1.00[AFR][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes]
rs2292937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs35832738	1.00[AFR][1000 genomes]
rs3735141	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62465483	1.00[AFR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes]
rs62465545	1.00[AFR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes]
rs62467382	1.00[AFR][1000 genomes]
rs62467384	1.00[AFR][1000 genomes]
rs62467385	1.00[AFR][1000 genomes]
rs62467386	1.00[AFR][1000 genomes]
rs62467410	1.00[AFR][1000 genomes]
rs62467411	1.00[AFR][1000 genomes]
rs62467413	1.00[AFR][1000 genomes]
rs62467414	1.00[AFR][1000 genomes]
rs62467421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62467436	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62467437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62467441	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62467442	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62467444	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62467450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes]
rs62468673	1.00[AFR][1000 genomes]
rs62468674	1.00[AFR][1000 genomes]
rs62468677	1.00[AFR][1000 genomes]
rs62468679	1.00[AFR][1000 genomes]
rs62470879	1.00[AFR][1000 genomes]
rs62470880	1.00[AFR][1000 genomes]
rs62470886	1.00[AFR][1000 genomes]
rs62470891	1.00[AFR][1000 genomes]
rs62470894	1.00[AFR][1000 genomes]
rs62470895	1.00[AFR][1000 genomes]
rs62470897	1.00[AFR][1000 genomes]
rs62470899	1.00[AFR][1000 genomes]
rs62470900	1.00[AFR][1000 genomes]
rs62470921	1.00[AFR][1000 genomes]
rs62470922	1.00[AFR][1000 genomes]
rs62470924	1.00[AFR][1000 genomes]
rs62470925	1.00[AFR][1000 genomes]
rs62470926	1.00[AFR][1000 genomes]
rs62470931	1.00[AFR][1000 genomes]
rs62470934	1.00[AFR][1000 genomes]
rs62470940	1.00[AFR][1000 genomes]
rs62470945	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12530898	RABGEF1	cis	multi-tissue	Pritchard
rs12530898	hmm32897	cis	multi-tissue	Pritchard
rs12530898	RABGEF1	cis	lymphoblastoid	seeQTL
rs12530898	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65541600-65565000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:65541800-65554200	Weak transcription	HSMMtube	muscle
3	chr7:65541800-65556800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:65541800-65564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr7:65541800-65564600	Weak transcription	Fetal Brain Female	brain
6	chr7:65541800-65564800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:65542000-65552000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:65542000-65553400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:65542000-65553600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:65542000-65554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:65542000-65559600	Weak transcription	Psoas Muscle	Psoas
12	chr7:65542000-65564600	Weak transcription	Primary B cells from cord blood	blood
13	chr7:65542000-65564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:65542000-65564800	Weak transcription	Aorta	Aorta
15	chr7:65542000-65564800	Weak transcription	HSMM	muscle
16	chr7:65542200-65551800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr7:65542200-65552000	Weak transcription	HUVEC	blood vessel
18	chr7:65542200-65556000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:65542200-65564600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:65542200-65564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:65542200-65564600	Weak transcription	Brain Angular Gyrus	brain
22	chr7:65542200-65564600	Weak transcription	Fetal Kidney	kidney
23	chr7:65542200-65564600	Weak transcription	NH-A	brain
24	chr7:65542200-65564800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr7:65542400-65556200	Weak transcription	Osteobl	bone
26	chr7:65542400-65564400	Weak transcription	Hela-S3	cervix
27	chr7:65542800-65560600	Strong transcription	Fetal Stomach	stomach
28	chr7:65543000-65551800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65543000-65564600	Weak transcription	NHDF-Ad	bronchial
30	chr7:65543200-65554600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:65543200-65564400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr7:65543400-65551400	Weak transcription	Placenta	Placenta
33	chr7:65543400-65558600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:65543400-65558600	Weak transcription	Small Intestine	intestine
35	chr7:65543400-65559200	Strong transcription	Fetal Intestine Large	intestine
36	chr7:65543600-65561400	Strong transcription	Fetal Intestine Small	intestine
37	chr7:65544000-65553000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:65544200-65554000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:65544400-65551600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:65545600-65553200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr7:65545600-65554800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:65545600-65558200	Strong transcription	Lung	lung
43	chr7:65545800-65554400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:65546000-65552800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr7:65546000-65555400	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr7:65546200-65560600	Strong transcription	Liver	Liver
47	chr7:65546400-65554400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr7:65546400-65559000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr7:65546600-65552800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:65546600-65553800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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