Variant report

Variant	rs1923279
Chromosome Location	chr6:38099195-38099196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10755700	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1979759	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2201646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4506034	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4714123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4714125	0.85[ASN][1000 genomes]
rs6458040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6458042	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6916091	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917668	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs6924634	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6929371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6930859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs6936504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938580	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]
rs7751390	0.94[ASN][1000 genomes]
rs7765798	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs881681	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs9349053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9369029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs9369033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380716	0.84[ASN][1000 genomes]
rs9462374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs9462380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9470762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9470767	0.94[ASN][1000 genomes]
rs9470800	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];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

No data

Chromatin state (count:107 , 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	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
4	chr6:38060000-38108200	Weak transcription	Ovary	ovary
5	chr6:38072200-38108400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:38075200-38118200	Weak transcription	Colonic Mucosa	Colon
7	chr6:38075400-38103800	Weak transcription	Pancreas	Pancrea
8	chr6:38076600-38104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:38078800-38109000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:38078800-38111000	Weak transcription	Fetal Kidney	kidney
11	chr6:38078800-38111000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:38079600-38113800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:38080400-38104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:38081800-38121800	Weak transcription	Psoas Muscle	Psoas
15	chr6:38083800-38103800	Weak transcription	Esophagus	oesophagus
16	chr6:38084000-38122200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:38084600-38124200	Weak transcription	Hela-S3	cervix
18	chr6:38085800-38099400	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:38086400-38099200	Weak transcription	NHLF	lung
20	chr6:38086600-38102400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:38087200-38101600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:38087600-38099400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:38087600-38100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:38087600-38101800	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:38087600-38103800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:38087600-38104800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:38087600-38118800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:38087800-38104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:38088000-38102200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:38088000-38104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:38088600-38099200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:38089200-38100000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:38089200-38103800	Weak transcription	Gastric	stomach
34	chr6:38089600-38106200	Weak transcription	Placenta	Placenta
35	chr6:38089800-38099400	Weak transcription	Left Ventricle	heart
36	chr6:38090000-38111000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:38090200-38099200	Weak transcription	Adipose Nuclei	Adipose
38	chr6:38090400-38106200	Weak transcription	NHEK	skin
39	chr6:38091200-38099200	Weak transcription	HSMM	muscle
40	chr6:38091200-38106200	Weak transcription	Dnd41	blood
41	chr6:38091200-38119800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:38091400-38100400	Weak transcription	HepG2	liver
43	chr6:38091400-38109400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:38091400-38110200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:38091400-38110400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:38091400-38116000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:38091400-38141800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:38091600-38101000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr6:38091800-38107200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:38091800-38109600	Weak transcription	Fetal Muscle Trunk	muscle

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