Variant report

Variant	rs831499
Chromosome Location	chr6:36990736-36990737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36989173..36991551-chr6:37137394..37139647,3	K562	blood:
2	chr6:36990423..36992455-chr6:37172095..37173787,2	K562	blood:
3	chr6:36989570..36992539-chr6:37178142..37179821,2	MCF-7	breast:
4	chr6:36990365..36993008-chr6:37173056..37174910,2	MCF-7	breast:
5	chr6:36989505..36991415-chr6:36995722..36997546,2	K562	blood:
6	chr6:36989418..36991271-chr6:36992892..36995334,2	K562	blood:
7	chr6:36990515..36993191-chr6:37140306..37142032,2	K562	blood:
8	chr6:36990051..36995346-chr6:37136390..37139647,6	K562	blood:
9	chr6:36989691..36991271-chr6:36992892..36995062,3	K562	blood:
10	chr6:36952740..36955730-chr6:36990686..36992977,2	MCF-7	breast:
11	chr6:36989705..36991355-chr6:37177906..37180017,2	K562	blood:
12	chr6:36989372..36991434-chr6:37069040..37071610,2	MCF-7	breast:
13	chr6:36990312..36994052-chr6:36999183..37001742,4	MCF-7	breast:
14	chr6:36990146..36994003-chr6:37137207..37141161,5	MCF-7	breast:
15	chr6:36990308..36994435-chr6:37135955..37142463,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1224487	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1224488	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1224491	0.95[ASN][1000 genomes]
rs1228575	0.97[ASN][1000 genomes]
rs1547571	0.81[EUR][1000 genomes]
rs1724094	0.95[ASN][1000 genomes]
rs1753300	0.80[ASN][1000 genomes]
rs1753301	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2025998	0.97[ASN][1000 genomes]
rs2094575	0.83[ASN][1000 genomes]
rs2149336	0.80[ASN][1000 genomes]
rs4317401	0.97[ASN][1000 genomes]
rs4711482	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457974	0.97[ASN][1000 genomes]
rs6457976	0.82[ASN][1000 genomes]
rs6457978	0.83[ASN][1000 genomes]
rs6924660	0.83[ASN][1000 genomes]
rs6939869	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748291	0.82[ASN][1000 genomes]
rs7750403	0.85[ASN][1000 genomes]
rs7750614	0.83[ASN][1000 genomes]
rs7750717	0.83[ASN][1000 genomes]
rs7770544	0.80[ASN][1000 genomes]
rs831484	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831487	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831489	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831491	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs831497	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831500	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831502	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913499	0.82[ASN][1000 genomes]
rs913500	0.90[ASN][1000 genomes]
rs913501	0.80[ASN][1000 genomes]
rs9296207	0.91[ASN][1000 genomes]
rs9296208	0.83[ASN][1000 genomes]
rs9366927	0.85[ASN][1000 genomes]
rs9380637	0.97[ASN][1000 genomes]
rs9394401	0.82[ASN][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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv885816	chr6:36965099-36999682	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3436059	chr6:36986674-36990872	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs831499	FGD2	cis	Skin Sun Exposed Lower leg	GTEx
rs831499	FGD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36983400-36995000	Weak transcription	Lung	lung
2	chr6:36986600-36991000	Weak transcription	Stomach Mucosa	stomach
3	chr6:36986600-36992600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:36986800-37006600	Weak transcription	Colonic Mucosa	Colon
5	chr6:36987000-36991200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:36987000-36991800	Strong transcription	GM12878-XiMat	blood
7	chr6:36987000-36993200	Weak transcription	Placenta	Placenta
8	chr6:36987000-36996800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:36987000-36996800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:36987200-36993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:36987200-36995000	Strong transcription	Primary B cells from cord blood	blood
12	chr6:36987200-36997200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:36987600-36991600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:36988200-36991400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:36988200-36998000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr6:36988600-36991600	Enhancers	Dnd41	blood
17	chr6:36988600-37006600	Weak transcription	Fetal Intestine Small	intestine
18	chr6:36988800-36991200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:36988800-36991600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:36989000-36990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:36989000-36992600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:36989200-36991000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:36989200-36991600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:36989200-36991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:36989200-36991800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:36989200-36992400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:36989200-36993400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:36989400-36991000	Enhancers	A549	lung
29	chr6:36989400-36991200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:36989400-36991400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:36989400-36991400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:36989400-36991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr6:36989400-36993000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:36989400-36994200	Enhancers	HMEC	breast
35	chr6:36989600-36992400	Enhancers	HepG2	liver
36	chr6:36989600-36993600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:36989800-36992600	Enhancers	Liver	Liver
38	chr6:36990000-36991000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:36990000-36991400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:36990000-36991400	Enhancers	Pancreas	Pancrea
41	chr6:36990000-36991400	Weak transcription	Hela-S3	cervix
42	chr6:36990000-36991800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:36990000-36992600	Weak transcription	HSMM	muscle
44	chr6:36990000-36992800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:36990000-36993400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:36990000-36993800	Weak transcription	K562	blood
47	chr6:36990000-36997000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:36990200-36991600	Strong transcription	Adipose Nuclei	Adipose
49	chr6:36990200-36994200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:36990200-36996400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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