Variant report

Variant	rs16883896
Chromosome Location	chr6:34255631-34255632
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34204148..34206580-chr6:34255031..34257952,2	K562	blood:
2	chr6:34254295..34258176-chr6:34263352..34265255,3	K562	blood:
3	chr6:34255342..34257076-chr6:34270066..34272272,2	K562	blood:
4	chr6:34213440..34216386-chr6:34253142..34255941,3	K562	blood:
5	chr6:34253947..34257801-chr6:34358558..34360626,3	K562	blood:
6	chr6:34251466..34254255-chr6:34254972..34256784,2	MCF-7	breast:
7	chr6:34253205..34255881-chr6:34257864..34260109,2	K562	blood:
8	chr6:34255111..34257575-chr6:34393125..34395055,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270800	Chromatin interaction
ENSG00000124614	Chromatin interaction
ENSG00000272325	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10484267	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057691	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060308	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10648	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127084	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13466	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883137	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883475	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888452	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628798	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.80[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269032	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269038	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55684754	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55694290	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779010	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833185	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864834	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56039915	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56107559	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274913	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309550	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738665	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7760373	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770443	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs875274	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[EUR][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	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16883896	NUDT3	cis	lymphoblastoid	seeQTL
rs16883896	LEMD2	cis	brain	seeQTL
rs16883896	ME1	trans	lymphoblastoid	seeQTL
rs16883896	NUDT3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34238400-34259400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
6	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
7	chr6:34243600-34257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:34244200-34260000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:34244400-34256600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:34245000-34259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:34245000-34260000	Weak transcription	NH-A	brain
13	chr6:34245000-34262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:34245000-34263400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:34245200-34259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:34245200-34260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:34245400-34260800	Weak transcription	Aorta	Aorta
18	chr6:34245600-34257400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:34245600-34261600	Weak transcription	Gastric	stomach
20	chr6:34245800-34260000	Weak transcription	HSMMtube	muscle
21	chr6:34246000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:34246600-34256800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:34246600-34264000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:34246600-34264000	Strong transcription	Dnd41	blood
25	chr6:34247200-34259600	Weak transcription	Fetal Heart	heart
26	chr6:34247400-34256400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:34247400-34259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:34247800-34260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:34248200-34256400	Weak transcription	Hela-S3	cervix
30	chr6:34249200-34259400	Weak transcription	Lung	lung
31	chr6:34249400-34259800	Weak transcription	Fetal Lung	lung
32	chr6:34249600-34257200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:34250000-34257800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr6:34250400-34256600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:34250600-34261000	Weak transcription	Colonic Mucosa	Colon
36	chr6:34250800-34256800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr6:34251000-34256400	Weak transcription	HUVEC	blood vessel
38	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:34251400-34256600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:34251600-34257400	Enhancers	Brain Angular Gyrus	brain
41	chr6:34252000-34256000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:34252000-34256200	Weak transcription	Spleen	Spleen
43	chr6:34252000-34256800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:34252200-34259800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:34252200-34259800	Weak transcription	Fetal Brain Male	brain
46	chr6:34252600-34257000	Strong transcription	Brain Germinal Matrix	brain
47	chr6:34253000-34256200	Weak transcription	Fetal Intestine Small	intestine
48	chr6:34253000-34256200	Weak transcription	Thymus	Thymus
49	chr6:34253000-34256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:34253000-34259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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