Variant report

Variant	rs12550765
Chromosome Location	chr8:95863360-95863361
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	chr8:95834166..95836580-chr8:95861416..95864115,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164941	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10091683	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10112232	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs10441538	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10956928	0.82[ASW][hapmap];0.97[GIH][hapmap];0.87[YRI][hapmap]
rs10956929	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10956930	0.88[CEU][hapmap]
rs10956931	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs10956932	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs1129152	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11784717	0.82[CEU][hapmap]
rs11988818	0.84[ASN][1000 genomes]
rs11996455	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs12541990	0.82[CEU][hapmap]
rs12545596	0.84[YRI][hapmap]
rs12548999	0.83[CEU][hapmap]
rs12677346	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13271375	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs13271644	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2123647	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs2278891	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2924477	0.83[EUR][1000 genomes]
rs2945554	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs2956216	0.91[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs3019175	0.88[CEU][hapmap]
rs3019182	0.90[EUR][1000 genomes]
rs35106232	0.86[ASN][1000 genomes]
rs4075835	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4076061	0.85[ASN][1000 genomes]
rs4735310	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4735312	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4735328	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4735331	0.88[CEU][hapmap]
rs4735332	0.88[CEU][hapmap]
rs4735334	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs477653	0.91[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes]
rs5002591	0.82[ASN][1000 genomes]
rs535322	0.90[EUR][1000 genomes]
rs550418	0.87[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs550564	0.91[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs551270	0.87[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs61537129	0.90[EUR][1000 genomes]
rs6471497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6471498	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471499	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap]
rs6471500	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6471501	0.80[EUR][1000 genomes]
rs6471504	0.93[CHB][hapmap]
rs683832	0.91[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6983000	0.84[YRI][hapmap]
rs6987256	0.82[ASW][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.84[YRI][hapmap]
rs6991067	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs6998921	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7002058	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7004862	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs7005317	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7013163	0.86[EUR][1000 genomes]
rs7015841	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs7017487	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs713113	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7817845	0.84[ASN][1000 genomes]
rs7820818	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs7839728	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9643348	0.85[ASN][1000 genomes]

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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12550765	TP53INP1	cis	multi-tissue	Pritchard
rs12550765	SLC26A7	cis	parietal	SCAN
rs12550765	INTS8	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95836800-95866800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:95836800-95874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:95837000-95905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:95837400-95898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:95837600-95869800	Weak transcription	Psoas Muscle	Psoas
6	chr8:95838200-95905600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:95838800-95876000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:95839400-95872200	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr8:95839400-95872400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:95839400-95872400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr8:95839400-95872400	Strong transcription	Dnd41	blood
12	chr8:95839400-95872600	Strong transcription	Liver	Liver
13	chr8:95839400-95872600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr8:95839400-95904400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:95839600-95873400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr8:95839600-95873400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr8:95840600-95873000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:95845800-95872600	Strong transcription	Placenta	Placenta
19	chr8:95847400-95873000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:95847400-95890800	Weak transcription	Stomach Mucosa	stomach
21	chr8:95848400-95873000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:95848800-95869000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:95849800-95872200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:95849800-95873000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:95850400-95872600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr8:95850600-95872600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr8:95851200-95866000	Weak transcription	NHLF	lung
28	chr8:95851400-95869000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr8:95851400-95870000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr8:95851400-95871800	Weak transcription	Fetal Heart	heart
31	chr8:95851600-95874200	Weak transcription	Pancreas	Pancrea
32	chr8:95852200-95866200	Weak transcription	Colonic Mucosa	Colon
33	chr8:95852400-95867000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:95852600-95865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:95854000-95866000	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:95854600-95872400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr8:95855400-95864400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr8:95855400-95865600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr8:95855400-95866000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr8:95855400-95867000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr8:95855600-95873800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr8:95855600-95874200	Strong transcription	Fetal Thymus	thymus
43	chr8:95855800-95873000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr8:95856000-95865600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr8:95856200-95864000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr8:95856200-95865600	Weak transcription	Hela-S3	cervix
47	chr8:95856200-95866600	Weak transcription	Brain Substantia Nigra	brain
48	chr8:95856200-95866800	Weak transcription	HepG2	liver
49	chr8:95856200-95868000	Weak transcription	Fetal Brain Male	brain
50	chr8:95856800-95866000	Weak transcription	Ovary	ovary

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