Variant report

Variant	rs3999791
Chromosome Location	chr6:87923487-87923488
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1145713	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1145714	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1145715	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1145716	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11759727	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1188806	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1203162	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1203163	0.81[ASN][1000 genomes]
rs1203164	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13201289	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13210074	0.84[EUR][1000 genomes]
rs16878497	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1746444	0.81[EUR][1000 genomes]
rs1753152	0.82[EUR][1000 genomes]
rs1925686	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2025490	0.85[EUR][1000 genomes]
rs2236048	0.82[EUR][1000 genomes]
rs242274	0.81[EUR][1000 genomes]
rs242275	0.81[EUR][1000 genomes]
rs242276	0.81[EUR][1000 genomes]
rs242282	0.82[EUR][1000 genomes]
rs2983136	0.82[EUR][1000 genomes]
rs368267	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs374792	0.81[EUR][1000 genomes]
rs382956	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs384318	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs385210	0.81[EUR][1000 genomes]
rs3857486	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411606	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs413687	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs414453	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235830	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707344	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707345	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4707355	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6908834	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913159	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6921673	0.82[ASN][1000 genomes]
rs6926686	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6932641	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6938885	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6939075	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6940325	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7752414	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757330	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7758360	0.93[ASN][1000 genomes]
rs7767245	0.83[EUR][1000 genomes]
rs827433	0.81[ASN][1000 genomes]
rs912815	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294375	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9294376	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9444476	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9444481	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444486	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9444488	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9444490	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9444491	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450619	0.85[EUR][1000 genomes]
rs9450623	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450630	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450637	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450638	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450639	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9450640	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9450646	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450651	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450653	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3999791	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs3999791	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs3999791	C6orf163	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
2	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
3	chr6:87881400-87926200	Weak transcription	Liver	Liver
4	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
5	chr6:87884000-87964400	Weak transcription	NHEK	skin
6	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
7	chr6:87889800-87926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:87890800-87933000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:87891200-87929200	Weak transcription	Thymus	Thymus
11	chr6:87891400-87932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:87894800-87924200	Weak transcription	Adipose Nuclei	Adipose
13	chr6:87894800-87926200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:87895800-87924000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:87896000-87932800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:87896400-87925600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:87896400-87926000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:87896400-87927400	Weak transcription	HMEC	breast
19	chr6:87896400-87927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:87896600-87925600	Weak transcription	HSMM	muscle
21	chr6:87905200-87950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:87906200-87956200	Weak transcription	A549	lung
23	chr6:87906400-87964400	Weak transcription	NHLF	lung
24	chr6:87907400-87930800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:87907800-87929200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:87909000-87928400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:87909000-87929800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:87910200-87934400	Weak transcription	Fetal Brain Male	brain
29	chr6:87910600-87956000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:87910800-87926000	Weak transcription	Osteobl	bone
31	chr6:87910800-87932800	Weak transcription	Aorta	Aorta
32	chr6:87911000-87925600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:87911200-87926000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:87913200-87925200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:87913600-87932800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:87913600-87932800	Weak transcription	Lung	lung
37	chr6:87913600-87934800	Weak transcription	Spleen	Spleen
38	chr6:87915200-87925800	Weak transcription	HUVEC	blood vessel
39	chr6:87915200-87929200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:87915600-87924800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:87916000-87927400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:87916200-87924800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr6:87916200-87928200	Weak transcription	NH-A	brain
44	chr6:87916800-87925600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:87916800-87926000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:87918200-87924600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:87918800-87932600	Weak transcription	Fetal Heart	heart
48	chr6:87919400-87931800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:87920000-87926600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:87920000-87945400	Strong transcription	Dnd41	blood

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