Variant report

Variant	rs11783878
Chromosome Location	chr8:95979261-95979262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95972771..95975327-chr8:95979134..95982751,4	MCF-7	breast:
2	chr8:95977216..95979367-chr8:95979972..95982886,3	K562	blood:
3	chr8:95958611..95965751-chr8:95975918..95982196,8	MCF-7	breast:
4	chr8:95977560..95980300-chr8:96031568..96033219,2	MCF-7	breast:
5	chr8:95979244..95983291-chr8:95999970..96003553,4	MCF-7	breast:
6	chr8:95959560..95963083-chr8:95975054..95981497,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164938	Chromatin interaction
ENSG00000253878	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10086541	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs10092003	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs10093594	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs10096455	0.81[CEU][hapmap]
rs10097930	0.81[CEU][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap]
rs10098025	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10098197	0.81[CEU][hapmap]
rs10098453	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs10111154	0.81[CEU][hapmap];0.89[CHD][hapmap];0.89[TSI][hapmap]
rs10504939	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]
rs10956927	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11774085	0.81[AFR][1000 genomes]
rs11775475	0.82[CEU][hapmap]
rs11776186	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11776189	0.81[CEU][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap]
rs11777353	1.00[JPT][hapmap]
rs11778553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11779282	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11779506	0.81[CHD][hapmap];1.00[LWK][hapmap]
rs11779698	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11780130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11780931	0.81[CEU][hapmap];0.89[CHD][hapmap];0.81[TSI][hapmap]
rs11781040	0.81[CEU][hapmap]
rs11781397	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11781429	1.00[JPT][hapmap]
rs11781757	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11782590	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11782617	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11782818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11783262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11783522	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs11783589	1.00[JPT][hapmap]
rs11783941	1.00[JPT][hapmap]
rs11783985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11784140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11784212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11784299	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11786021	1.00[JPT][hapmap]
rs11786088	1.00[JPT][hapmap]
rs11786389	1.00[JPT][hapmap]
rs11787303	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12056517	1.00[JPT][hapmap]
rs13250762	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1545480	0.89[CHD][hapmap]
rs16893774	0.82[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16917079	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs16917081	1.00[JPT][hapmap]
rs16917082	1.00[JPT][hapmap]
rs16917093	1.00[JPT][hapmap]
rs16917102	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs16917106	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs16917117	0.94[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs16917233	0.81[CEU][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap]
rs17359493	1.00[JPT][hapmap]
rs17665714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17665737	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17719449	1.00[ASW][hapmap]
rs2678823	0.89[CHD][hapmap]
rs28399553	0.87[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs2904889	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3802191	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3802192	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4075834	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4323442	0.81[CEU][hapmap]
rs4345531	1.00[JPT][hapmap]
rs57890591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58282276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58314911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60003497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61591488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471505	0.81[CEU][hapmap]
rs6651271	0.81[CEU][hapmap]
rs6651272	0.81[CEU][hapmap];0.89[CHD][hapmap];0.85[TSI][hapmap]
rs6986418	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs6989591	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7009940	0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs716733	0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7812312	0.81[CEU][hapmap];0.89[CHD][hapmap];0.89[TSI][hapmap]
rs7826196	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7834966	0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs7844932	0.92[GIH][hapmap]
rs896848	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297950	0.81[CEU][hapmap]
rs9297951	0.81[CHD][hapmap];0.85[TSI][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11783878	C8orf38	cis	cerebellum	SCAN
rs11783878	INTS8	cis	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95962800-95979800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr8:95962800-95980200	Weak transcription	Ovary	ovary
3	chr8:95962800-95980600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:95963000-95980400	Weak transcription	HSMM	muscle
5	chr8:95963600-95979600	Weak transcription	A549	lung
6	chr8:95963800-95979400	Weak transcription	Colon Smooth Muscle	Colon
7	chr8:95964400-95980000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:95964400-96002200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:95964600-95979400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:95964600-95980200	Weak transcription	Brain Substantia Nigra	brain
11	chr8:95964600-95980600	Weak transcription	Fetal Brain Female	brain
12	chr8:95964600-95992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:95964800-95980400	Weak transcription	Brain Anterior Caudate	brain
14	chr8:95964800-95981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:95964800-95999000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:95964800-95999600	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:95964800-95999600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr8:95965000-95999600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr8:95966000-95986800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr8:95966000-95993000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:95970600-96000800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:95971400-95986800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr8:95971400-95987400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr8:95971600-95979800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:95971600-95983800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:95971600-95987000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr8:95971600-95987000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:95971600-95987200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:95971600-96000400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr8:95971800-95986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:95972400-95980800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr8:95972400-95994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr8:95972600-95987600	Weak transcription	HMEC	breast
34	chr8:95972800-95980200	Weak transcription	Fetal Lung	lung
35	chr8:95973000-95980200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:95973000-95987000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr8:95973200-95980200	Weak transcription	HSMMtube	muscle
38	chr8:95973600-95979600	Weak transcription	NHEK	skin
39	chr8:95973600-95980200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr8:95973600-95981800	Enhancers	Pancreas	Pancrea
41	chr8:95974400-95979400	Weak transcription	NH-A	brain
42	chr8:95974400-95980200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr8:95974400-95980200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr8:95974400-96002000	Weak transcription	Esophagus	oesophagus
45	chr8:95974600-95979400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr8:95974600-95979400	Weak transcription	K562	blood
47	chr8:95974600-95980200	Weak transcription	Gastric	stomach
48	chr8:95974600-95980600	Weak transcription	Colonic Mucosa	Colon
49	chr8:95974600-95987000	Weak transcription	Thymus	Thymus
50	chr8:95975800-95981000	Enhancers	Osteobl	bone

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