Variant report

Variant	rs6938580
Chromosome Location	chr6:38091390-38091391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10755700	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198420	0.86[CHB][hapmap]
rs1885325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1923279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979759	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2201646	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs259687	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4506034	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4714123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4714125	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6458040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458042	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6916091	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917668	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6924634	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929371	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6930859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6936504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751390	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7765798	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs881681	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9349053	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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9369033	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380716	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9462374	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9462380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9470762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470767	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9470800	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6938580	TRERF1	cis	cerebellum	SCAN
rs6938580	LRFN2	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:38057200-38109200	Weak transcription	K562	blood
3	chr6:38059800-38091600	Weak transcription	Spleen	Spleen
4	chr6:38060000-38092000	Weak transcription	Aorta	Aorta
5	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
6	chr6:38060000-38108200	Weak transcription	Ovary	ovary
7	chr6:38063800-38099000	Weak transcription	NH-A	brain
8	chr6:38071800-38091400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:38072200-38108400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:38075200-38092000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:38075200-38118200	Weak transcription	Colonic Mucosa	Colon
12	chr6:38075400-38103800	Weak transcription	Pancreas	Pancrea
13	chr6:38076400-38091400	Strong transcription	Primary B cells from cord blood	blood
14	chr6:38076600-38104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:38078800-38099000	Weak transcription	NHDF-Ad	bronchial
16	chr6:38078800-38109000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:38078800-38111000	Weak transcription	Fetal Kidney	kidney
18	chr6:38078800-38111000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:38079600-38113800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:38080400-38104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:38081800-38121800	Weak transcription	Psoas Muscle	Psoas
22	chr6:38082600-38094400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:38082800-38091600	Strong transcription	Primary T cells from cord blood	blood
24	chr6:38083200-38095800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:38083400-38091600	Weak transcription	Small Intestine	intestine
26	chr6:38083600-38091400	Strong transcription	HepG2	liver
27	chr6:38083600-38092600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:38083600-38094000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr6:38083800-38091600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:38083800-38092000	Strong transcription	Fetal Thymus	thymus
31	chr6:38083800-38103800	Weak transcription	Esophagus	oesophagus
32	chr6:38084000-38122200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:38084200-38091400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:38084200-38091600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:38084200-38092200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:38084200-38095200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:38084400-38091400	Strong transcription	Liver	Liver
38	chr6:38084400-38092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:38084400-38092200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:38084600-38092000	Weak transcription	Lung	lung
41	chr6:38084600-38124200	Weak transcription	Hela-S3	cervix
42	chr6:38084800-38092400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:38085400-38093800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:38085600-38092000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:38085800-38099400	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:38086000-38092400	Weak transcription	HUVEC	blood vessel
47	chr6:38086200-38093400	Weak transcription	A549	lung
48	chr6:38086400-38099200	Weak transcription	NHLF	lung
49	chr6:38086600-38102400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:38086800-38092400	Weak transcription	Thymus	Thymus

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