Variant report

Variant	rs11776602
Chromosome Location	chr8:99014295-99014296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99011784..99014375-chr8:99051357..99053193,2	MCF-7	breast:
2	chr8:98880331..98882636-chr8:99012826..99014648,3	MCF-7	breast:
3	chr8:98852045..98852568-chr8:99013936..99014703,2	MCF-7	breast:
4	chr8:99014119..99017352-chr8:99021059..99024142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10098159	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955140	0.85[CEU][hapmap]
rs10955141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955142	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955143	0.85[CEU][hapmap]
rs10955145	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955147	0.86[ASN][1000 genomes]
rs11559201	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11559202	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11777189	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785807	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11990341	0.83[ASN][1000 genomes]
rs11991161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11996042	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11997426	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12544193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549967	1.00[ASN][1000 genomes]
rs12550104	1.00[ASN][1000 genomes]
rs13248865	1.00[ASN][1000 genomes]
rs13254615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255477	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265127	1.00[ASN][1000 genomes]
rs13268951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13269757	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13270713	0.85[CEU][hapmap]
rs13274382	1.00[ASN][1000 genomes]
rs13279197	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13439743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17829645	1.00[JPT][hapmap]
rs2279120	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088121	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34139241	1.00[ASN][1000 genomes]
rs34276726	1.00[ASN][1000 genomes]
rs34899856	1.00[ASN][1000 genomes]
rs35170774	0.86[EUR][1000 genomes]
rs35417638	1.00[ASN][1000 genomes]
rs3758031	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.97[ASN][1000 genomes]
rs55779959	1.00[ASN][1000 genomes]
rs56137923	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57866232	1.00[ASN][1000 genomes]
rs60324498	1.00[ASN][1000 genomes]
rs68116021	0.83[ASN][1000 genomes]
rs68131553	1.00[ASN][1000 genomes]
rs6985709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6986891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004993	1.00[ASN][1000 genomes]
rs7012838	1.00[ASN][1000 genomes]
rs7016999	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71514975	1.00[ASN][1000 genomes]
rs72678742	1.00[ASN][1000 genomes]
rs812	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv528695	chr8:98960813-99022009	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11776602	TSPYL5	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98992600-99019400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:98994200-99014800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:99008200-99015400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
5	chr8:99008800-99014800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr8:99009000-99016800	Weak transcription	Placenta	Placenta
7	chr8:99009000-99030000	Weak transcription	Pancreas	Pancrea
8	chr8:99009000-99030200	Weak transcription	Esophagus	oesophagus
9	chr8:99009600-99022600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:99009800-99014400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:99009800-99014600	Weak transcription	Right Atrium	heart
12	chr8:99010000-99015400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:99011800-99015200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:99012000-99017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:99012000-99028800	Weak transcription	Aorta	Aorta
16	chr8:99012000-99032000	Weak transcription	Gastric	stomach
17	chr8:99012400-99014400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:99012400-99028800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr8:99013400-99015000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:99013400-99015000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:99013400-99015400	Enhancers	Brain Angular Gyrus	brain
22	chr8:99013600-99014800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:99013600-99015000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr8:99013800-99014800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr8:99013800-99015600	Enhancers	Brain Anterior Caudate	brain
26	chr8:99013800-99018600	Weak transcription	Fetal Intestine Small	intestine
27	chr8:99014000-99014400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr8:99014000-99014400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr8:99014000-99014400	Enhancers	A549	lung
30	chr8:99014000-99014600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:99014000-99014800	Enhancers	Adipose Nuclei	Adipose
32	chr8:99014000-99014800	Enhancers	Colon Smooth Muscle	Colon
33	chr8:99014000-99015000	Enhancers	NHLF	lung
34	chr8:99014000-99015000	Enhancers	Osteobl	bone
35	chr8:99014000-99015200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:99014000-99022400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr8:99014200-99014400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:99014200-99014400	Active TSS	Brain Hippocampus Middle	brain
39	chr8:99014200-99014400	Flanking Active TSS	Fetal Lung	lung
40	chr8:99014200-99014400	Flanking Active TSS	Hela-S3	cervix
41	chr8:99014200-99014400	Enhancers	HSMMtube	muscle
42	chr8:99014200-99014600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr8:99014200-99014600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr8:99014200-99014600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:99014200-99014600	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr8:99014200-99014600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr8:99014200-99014600	Enhancers	Stomach Smooth Muscle	stomach
48	chr8:99014200-99014600	Enhancers	HSMM	muscle
49	chr8:99014200-99014800	Enhancers	Fetal Stomach	stomach
50	chr8:99014200-99014800	Enhancers	Ovary	ovary

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