Variant report

Variant	rs3799109
Chromosome Location	chr6:70413118-70413119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10498869	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13437057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1457498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16868113	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16868129	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503698	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28434733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707375	0.90[ASN][1000 genomes]
rs6936974	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294846	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294847	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9294849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446157	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446159	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9446161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454865	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9454880	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454881	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454887	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454889	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454890	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9454892	0.88[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9454893	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv830682	chr6:70397851-70592883	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv970139	chr6:70412763-70416038	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70378800-70416800	Weak transcription	Fetal Kidney	kidney
2	chr6:70378800-70430800	Weak transcription	Fetal Stomach	stomach
3	chr6:70378800-70430800	Weak transcription	Spleen	Spleen
4	chr6:70378800-70435200	Weak transcription	Psoas Muscle	Psoas
5	chr6:70379000-70428400	Weak transcription	Ovary	ovary
6	chr6:70379000-70435400	Weak transcription	Fetal Brain Male	brain
7	chr6:70379600-70431000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:70380400-70430600	Weak transcription	Fetal Intestine Small	intestine
9	chr6:70380600-70455600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:70380800-70467800	Weak transcription	K562	blood
11	chr6:70382200-70435400	Weak transcription	Brain Angular Gyrus	brain
12	chr6:70382400-70430200	Weak transcription	Small Intestine	intestine
13	chr6:70383800-70431000	Weak transcription	Lung	lung
14	chr6:70384000-70415800	Weak transcription	Fetal Lung	lung
15	chr6:70384200-70428400	Weak transcription	Aorta	Aorta
16	chr6:70384200-70431000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:70384600-70417400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:70385000-70421600	Weak transcription	Fetal Intestine Large	intestine
19	chr6:70387600-70415600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:70388000-70423400	Weak transcription	Left Ventricle	heart
21	chr6:70397200-70415600	Weak transcription	Primary T cells from cord blood	blood
22	chr6:70397800-70439000	Weak transcription	Fetal Heart	heart
23	chr6:70398000-70423000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:70400800-70430800	Weak transcription	Pancreas	Pancrea
25	chr6:70402000-70430800	Weak transcription	Esophagus	oesophagus
26	chr6:70402200-70435200	Weak transcription	Brain Anterior Caudate	brain
27	chr6:70402800-70430800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:70403000-70429800	Weak transcription	NHDF-Ad	bronchial
29	chr6:70403200-70415400	Weak transcription	HSMM	muscle
30	chr6:70403400-70432200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:70403800-70422800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:70404200-70447400	Weak transcription	Hela-S3	cervix
33	chr6:70404400-70420000	Weak transcription	NHLF	lung
34	chr6:70404600-70433800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:70405000-70432200	Weak transcription	Fetal Brain Female	brain
36	chr6:70405000-70468400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:70405400-70434600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:70405600-70427600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:70405600-70446400	Weak transcription	HepG2	liver
40	chr6:70406000-70430800	Weak transcription	Thymus	Thymus
41	chr6:70406000-70433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:70406200-70438400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:70406600-70431200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:70406600-70449400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:70406600-70457400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:70408000-70422800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:70408000-70430200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:70408200-70415600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:70408200-70415600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr6:70408200-70416800	Weak transcription	Rectal Mucosa Donor 29	rectum

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