Variant report

Variant	rs6659939
Chromosome Location	chr1:179811936-179811937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179810244..179812885-chr1:179816877..179820145,3	K562	blood:
2	chr1:179807872..179810257-chr1:179811726..179814159,3	K562	blood:
3	chr1:179811427..179813189-chr1:179817420..179819115,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1048418	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10494523	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913895	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913905	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10913909	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12119431	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121694	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126625	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12136091	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12136465	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12143942	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12144991	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16854910	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3845388	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4301600	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61740391	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6425596	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6673144	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72708661	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72708662	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7527215	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531195	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545581	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549317	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9726605	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795200-179812400	Weak transcription	Left Ventricle	heart
2	chr1:179795200-179815200	Weak transcription	Ovary	ovary
3	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:179799600-179815200	Weak transcription	Brain Angular Gyrus	brain
6	chr1:179800400-179815200	Weak transcription	Psoas Muscle	Psoas
7	chr1:179800600-179815200	Weak transcription	Esophagus	oesophagus
8	chr1:179800800-179815200	Weak transcription	Hela-S3	cervix
9	chr1:179801000-179814400	Weak transcription	HMEC	breast
10	chr1:179801000-179815000	Weak transcription	K562	blood
11	chr1:179801200-179815200	Weak transcription	Lung	lung
12	chr1:179801200-179815200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:179801200-179815200	Weak transcription	Spleen	Spleen
14	chr1:179801600-179813200	Weak transcription	GM12878-XiMat	blood
15	chr1:179801800-179813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:179801800-179815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:179801800-179815200	Weak transcription	NHDF-Ad	bronchial
18	chr1:179802200-179815200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:179802400-179813400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:179802400-179815000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:179802400-179815200	Weak transcription	Thymus	Thymus
22	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:179802600-179814200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:179802600-179815200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:179802600-179819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:179802800-179813200	Weak transcription	Dnd41	blood
27	chr1:179802800-179813400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr1:179803200-179813400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:179803200-179813600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:179803200-179815200	Weak transcription	Brain Anterior Caudate	brain
31	chr1:179803400-179815200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:179803400-179815200	Weak transcription	Small Intestine	intestine
33	chr1:179803600-179813200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:179803600-179815000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:179803600-179815200	Weak transcription	Brain Germinal Matrix	brain
36	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
37	chr1:179803800-179814400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:179803800-179815000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:179804000-179815000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:179804000-179815000	Weak transcription	Fetal Lung	lung
41	chr1:179804200-179815400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:179805400-179813000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:179805400-179815200	Weak transcription	Aorta	Aorta
44	chr1:179805400-179815200	Weak transcription	Right Ventricle	heart
45	chr1:179805800-179815200	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:179805800-179818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:179806200-179814000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:179806200-179815000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:179806200-179817600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:179807000-179813600	Weak transcription	A549	lung

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