Variant report

Variant	rs55718117
Chromosome Location	chr6:12144489-12144490
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12143600..12146335-chr6:12290629..12293218,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16872277	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3734271	0.98[ASN][1000 genomes]
rs3777754	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777758	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777762	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907440	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916455	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928420	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6940075	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72826076	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72826081	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72826086	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826088	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826091	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751398	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366980	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369074	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9369101	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369106	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380837	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394540	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9394541	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12121400-12150200	Weak transcription	Fetal Brain Male	brain
2	chr6:12122200-12161800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:12128600-12148400	Weak transcription	Fetal Heart	heart
4	chr6:12134800-12149600	Weak transcription	Brain Angular Gyrus	brain
5	chr6:12137000-12163600	Weak transcription	Small Intestine	intestine
6	chr6:12138400-12148000	Weak transcription	Osteobl	bone
7	chr6:12138400-12148400	Weak transcription	Hela-S3	cervix
8	chr6:12138800-12148400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:12138800-12148400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:12138800-12148400	Weak transcription	NHLF	lung
11	chr6:12139000-12148000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:12139000-12148400	Weak transcription	HSMMtube	muscle
13	chr6:12139000-12154200	Weak transcription	Right Atrium	heart
14	chr6:12139000-12161600	Weak transcription	HepG2	liver
15	chr6:12139400-12148200	Weak transcription	HSMM	muscle
16	chr6:12139600-12147600	Weak transcription	A549	lung
17	chr6:12139600-12148000	Weak transcription	NHEK	skin
18	chr6:12139800-12149800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:12140000-12148400	Weak transcription	NHDF-Ad	bronchial
20	chr6:12140000-12154600	Weak transcription	Right Ventricle	heart
21	chr6:12140200-12161800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:12140400-12149800	Weak transcription	Brain Germinal Matrix	brain
23	chr6:12140400-12150200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:12140600-12147400	Weak transcription	K562	blood
25	chr6:12140600-12147800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:12140600-12148000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:12140600-12148200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:12140600-12148400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:12140600-12148400	Weak transcription	Left Ventricle	heart
30	chr6:12140600-12149800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:12140600-12149800	Weak transcription	Ovary	ovary
32	chr6:12140600-12151400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:12140600-12155400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:12140600-12158400	Weak transcription	Aorta	Aorta
35	chr6:12140600-12158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:12140600-12158800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:12140600-12161400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:12140600-12161400	Weak transcription	Pancreas	Pancrea
39	chr6:12140600-12161400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:12140600-12161400	Weak transcription	Spleen	Spleen
41	chr6:12140600-12161600	Weak transcription	Esophagus	oesophagus
42	chr6:12140600-12161800	Weak transcription	Gastric	stomach
43	chr6:12140600-12163600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:12140600-12163600	Weak transcription	Psoas Muscle	Psoas
45	chr6:12140600-12163800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr6:12140800-12144600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:12140800-12147000	Weak transcription	GM12878-XiMat	blood
48	chr6:12140800-12147000	Weak transcription	HUVEC	blood vessel
49	chr6:12140800-12147200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:12140800-12147200	Weak transcription	Fetal Thymus	thymus

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