Variant report

Variant	rs10504939
Chromosome Location	chr8:95983354-95983355
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:95975437..95977833-chr8:95982234..95984948,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10086541	0.81[CEU][hapmap]
rs10092003	0.81[CEU][hapmap]
rs10093594	0.81[CEU][hapmap]
rs10096455	1.00[CHB][hapmap]
rs10097930	0.81[CEU][hapmap]
rs10098025	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10098197	1.00[CHB][hapmap]
rs10098453	0.81[CEU][hapmap]
rs10111154	0.81[CEU][hapmap]
rs10111300	1.00[CHB][hapmap]
rs10113545	1.00[CHB][hapmap]
rs1031388	1.00[CHB][hapmap]
rs10956927	1.00[JPT][hapmap]
rs11774085	0.81[AFR][1000 genomes]
rs11775475	0.83[CEU][hapmap]
rs11776186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11776189	0.81[CEU][hapmap]
rs11777353	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11778553	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11779282	0.88[EUR][1000 genomes]
rs11779698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11780130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11780931	0.81[CEU][hapmap]
rs11781040	1.00[CHB][hapmap]
rs11781397	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11781429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11781757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782590	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11782617	1.00[JPT][hapmap]
rs11782818	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11783262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11783522	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11783589	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11783878	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11783941	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11783985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11784140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11784299	1.00[JPT][hapmap]
rs11786021	1.00[JPT][hapmap]
rs11786088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11786389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11787303	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12056517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13250762	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893774	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs16917079	1.00[JPT][hapmap]
rs16917081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16917082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16917093	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16917102	1.00[JPT][hapmap]
rs16917106	1.00[JPT][hapmap]
rs16917117	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs16917224	1.00[CHB][hapmap]
rs16917233	0.81[CEU][hapmap]
rs17359493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17665714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599711	1.00[CHB][hapmap]
rs28399553	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2904889	0.87[EUR][1000 genomes]
rs3802191	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075834	1.00[JPT][hapmap]
rs4323442	1.00[CHB][hapmap]
rs4345531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57890591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58282276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58314911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60003497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61591488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471505	1.00[CHB][hapmap]
rs6651271	1.00[CHB][hapmap]
rs6651272	0.81[CEU][hapmap]
rs6986418	1.00[JPT][hapmap]
rs6989591	1.00[JPT][hapmap]
rs7008542	1.00[CHB][hapmap]
rs7009940	1.00[JPT][hapmap]
rs716733	1.00[JPT][hapmap]
rs7812312	0.81[CEU][hapmap]
rs7826196	0.81[CEU][hapmap]
rs7834966	1.00[JPT][hapmap]
rs896848	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297950	1.00[CHB][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	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	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10504939	INTS8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95964400-96002200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:95964600-95992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:95964800-95999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:95964800-95999600	Weak transcription	Brain Hippocampus Middle	brain
5	chr8:95964800-95999600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:95965000-95999600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr8:95966000-95986800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:95966000-95993000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr8:95970600-96000800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:95971400-95986800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:95971400-95987400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:95971600-95983800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr8:95971600-95987000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr8:95971600-95987000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:95971600-95987200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr8:95971600-96000400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr8:95971800-95986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr8:95972400-95994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr8:95972600-95987600	Weak transcription	HMEC	breast
20	chr8:95973000-95987000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr8:95974400-96002000	Weak transcription	Esophagus	oesophagus
22	chr8:95974600-95987000	Weak transcription	Thymus	Thymus
23	chr8:95976200-95990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:95976600-95993200	Weak transcription	Primary T cells from cord blood	blood
25	chr8:95976800-95988800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr8:95977400-95989600	Weak transcription	Fetal Stomach	stomach
27	chr8:95977400-96024200	Weak transcription	Aorta	Aorta
28	chr8:95977600-96008800	Weak transcription	Brain Germinal Matrix	brain
29	chr8:95979200-95983800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr8:95979400-95986200	Weak transcription	Dnd41	blood
31	chr8:95979800-95986200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr8:95980400-95993200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:95980800-95986800	Weak transcription	Lung	lung
34	chr8:95980800-95986800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:95980800-95987200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr8:95980800-95988800	Weak transcription	Primary B cells from cord blood	blood
37	chr8:95980800-95993000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:95980800-95993000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr8:95980800-95993000	Weak transcription	HSMMtube	muscle
40	chr8:95980800-95993200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr8:95980800-95999400	Weak transcription	Brain Substantia Nigra	brain
42	chr8:95980800-95999600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr8:95980800-96000200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:95980800-96000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr8:95981000-95983400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr8:95981000-95983400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr8:95981000-95985000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr8:95981000-95986800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr8:95981000-95986800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr8:95981000-95988800	Weak transcription	Primary B cells from peripheral blood	blood

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