Variant report

Variant	rs9478780
Chromosome Location	chr6:151008994-151008995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:151007139..151009866-chr6:151010268..151011885,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10872666	0.84[AMR][1000 genomes]
rs12664686	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17080073	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17080108	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2345745	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4036092	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4869926	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4869927	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4869928	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4869929	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4869930	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4869931	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55646755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58824807	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59155780	0.91[AFR][1000 genomes]
rs59466561	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6899782	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6908127	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6929743	0.93[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73010188	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7738394	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs7749222	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs9478775	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9478783	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9480514	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9480526	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9480528	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9480529	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9480530	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9480531	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480533	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9885650	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9885699	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9885836	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150980800-151014800	Weak transcription	Pancreas	Pancrea
2	chr6:150990600-151016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:150990800-151011800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:151000800-151010000	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:151003600-151011400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:151003800-151015000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:151004800-151012000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:151005000-151017400	Weak transcription	Aorta	Aorta
9	chr6:151005800-151018400	Weak transcription	Psoas Muscle	Psoas
10	chr6:151006000-151018400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:151006600-151011400	Enhancers	Primary B cells from cord blood	blood
12	chr6:151006600-151011800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:151006600-151011800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:151006600-151014600	Weak transcription	Right Atrium	heart
15	chr6:151006800-151017200	Weak transcription	Fetal Stomach	stomach
16	chr6:151007000-151009400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:151007200-151011200	Weak transcription	GM12878-XiMat	blood
18	chr6:151007400-151014800	Weak transcription	Thymus	Thymus
19	chr6:151007600-151009800	Enhancers	Fetal Muscle Leg	muscle
20	chr6:151007800-151009000	Enhancers	Ovary	ovary
21	chr6:151008000-151009400	Enhancers	Fetal Intestine Large	intestine
22	chr6:151008000-151009800	Enhancers	Stomach Mucosa	stomach
23	chr6:151008000-151011400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:151008000-151011400	Weak transcription	Left Ventricle	heart
25	chr6:151008000-151012200	Enhancers	HUVEC	blood vessel
26	chr6:151008200-151009400	Enhancers	Fetal Lung	lung
27	chr6:151008200-151009600	Enhancers	Adipose Nuclei	Adipose
28	chr6:151008200-151009800	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr6:151008200-151011400	Weak transcription	Spleen	Spleen
30	chr6:151008400-151009400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:151008400-151009400	Enhancers	Duodenum Mucosa	Duodenum
32	chr6:151008400-151009400	Enhancers	Fetal Intestine Small	intestine
33	chr6:151008400-151012200	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:151008600-151009000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr6:151008600-151009000	Flanking Active TSS	Placenta	Placenta
36	chr6:151008600-151009200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:151008600-151009400	Enhancers	Brain Cingulate Gyrus	brain
38	chr6:151008600-151009400	Enhancers	Fetal Kidney	kidney
39	chr6:151008600-151009400	Enhancers	HepG2	liver
40	chr6:151008800-151009000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:151008800-151009000	Enhancers	Esophagus	oesophagus
42	chr6:151008800-151009000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:151008800-151009000	Enhancers	Fetal Muscle Trunk	muscle
44	chr6:151008800-151009000	Enhancers	Gastric	stomach
45	chr6:151008800-151009000	Genic enhancers	Lung	lung
46	chr6:151008800-151009000	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:151008800-151009400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr6:151008800-151009400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr6:151008800-151009400	Enhancers	Rectal Smooth Muscle	rectum
50	chr6:151008800-151009800	Enhancers	Small Intestine	intestine

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