Variant report

Variant	rs10955143
Chromosome Location	chr8:99016092-99016093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99015593..99019656-chr8:99049212..99053715,4	MCF-7	breast:
2	chr8:99006609..99009034-chr8:99014356..99016713,2	MCF-7	breast:
3	chr8:99014119..99017352-chr8:99021059..99024142,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10106983	0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs10955140	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10955141	0.85[CEU][hapmap]
rs10955144	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955146	0.85[CEU][hapmap]
rs11776602	0.85[CEU][hapmap]
rs11784449	0.85[CEU][hapmap]
rs11785807	0.85[CEU][hapmap]
rs12549307	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12676252	0.86[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs12680911	0.81[JPT][hapmap]
rs13254615	0.85[CEU][hapmap]
rs13254737	0.85[CEU][hapmap]
rs13270713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13439743	0.84[CEU][hapmap]
rs16896564	0.81[JPT][hapmap]
rs2034780	0.93[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs2290469	0.85[CEU][hapmap]
rs36191777	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4735521	0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs6985434	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6986891	0.85[CEU][hapmap]
rs6987112	0.85[CEU][hapmap]
rs7830701	0.81[JPT][hapmap]
rs7843262	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10955143	LAPTM4B	cis	lymphoblastoid	seeQTL
rs10955143	GRHL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98992600-99019400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
3	chr8:99009000-99016800	Weak transcription	Placenta	Placenta
4	chr8:99009000-99030000	Weak transcription	Pancreas	Pancrea
5	chr8:99009000-99030200	Weak transcription	Esophagus	oesophagus
6	chr8:99009600-99022600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:99012000-99017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:99012000-99028800	Weak transcription	Aorta	Aorta
9	chr8:99012000-99032000	Weak transcription	Gastric	stomach
10	chr8:99012400-99028800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr8:99013800-99018600	Weak transcription	Fetal Intestine Small	intestine
12	chr8:99014000-99022400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:99014200-99025400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr8:99014200-99029600	Weak transcription	Fetal Intestine Large	intestine
15	chr8:99014400-99018000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:99014600-99016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:99014600-99017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr8:99014600-99019600	Weak transcription	Liver	Liver
19	chr8:99014600-99019800	Weak transcription	Fetal Lung	lung
20	chr8:99014600-99020000	Weak transcription	HSMM	muscle
21	chr8:99014600-99021200	Enhancers	Brain Cingulate Gyrus	brain
22	chr8:99014600-99021400	Enhancers	Brain Hippocampus Middle	brain
23	chr8:99014800-99017400	Weak transcription	Ovary	ovary
24	chr8:99014800-99018000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:99014800-99018000	Weak transcription	Adipose Nuclei	Adipose
26	chr8:99014800-99018200	Weak transcription	NH-A	brain
27	chr8:99014800-99022600	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr8:99014800-99023000	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:99015000-99016600	Weak transcription	Osteobl	bone
30	chr8:99015000-99017200	Weak transcription	NHLF	lung
31	chr8:99015000-99017800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr8:99015000-99018200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr8:99015000-99019800	Weak transcription	NHDF-Ad	bronchial
34	chr8:99015000-99020000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:99015000-99034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr8:99015200-99016400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr8:99015200-99016600	Strong transcription	Fetal Stomach	stomach
38	chr8:99015200-99017000	Weak transcription	Right Atrium	heart
39	chr8:99015200-99022000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr8:99015200-99023600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr8:99015400-99016600	Weak transcription	Brain Angular Gyrus	brain
42	chr8:99015400-99016600	Weak transcription	Brain Substantia Nigra	brain
43	chr8:99015400-99016800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr8:99015400-99018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:99015400-99021200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr8:99015600-99016600	Weak transcription	Brain Anterior Caudate	brain
47	chr8:99015800-99016800	Enhancers	Fetal Muscle Trunk	muscle
48	chr8:99015800-99023800	Weak transcription	Spleen	Spleen
49	chr8:99016000-99016400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr8:99016000-99017400	Weak transcription	Duodenum Mucosa	Duodenum

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