Variant report

Variant	rs966946
Chromosome Location	chr8:126030809-126030810
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	chr8:126009436..126011531-chr8:126030679..126034606,3	MCF-7	breast:
2	chr8:126010242..126013491-chr8:126029890..126034767,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104549	Chromatin interaction
ENSG00000253513	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10086441	0.94[ASN][1000 genomes]
rs10087191	1.00[ASN][1000 genomes]
rs10087246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10102230	0.87[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs10103150	0.99[ASN][1000 genomes]
rs10216429	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10216437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10481152	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1156712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1156713	1.00[ASN][1000 genomes]
rs12542833	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12543024	0.99[ASN][1000 genomes]
rs12548159	0.98[ASN][1000 genomes]
rs12548192	0.88[CHB][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs12550607	0.84[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs12682006	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1319792	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13249949	1.00[ASN][1000 genomes]
rs13251808	1.00[ASN][1000 genomes]
rs13251846	0.99[ASN][1000 genomes]
rs13257850	1.00[ASN][1000 genomes]
rs13265195	0.91[ASN][1000 genomes]
rs16900177	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16900238	1.00[ASN][1000 genomes]
rs16900316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2033130	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2382998	0.91[ASN][1000 genomes]
rs2384921	0.83[CHB][hapmap]
rs28670937	0.89[ASN][1000 genomes]
rs28706061	0.81[ASN][1000 genomes]
rs28760092	1.00[ASN][1000 genomes]
rs28873392	1.00[ASN][1000 genomes]
rs36090120	0.92[ASN][1000 genomes]
rs3750234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3750235	1.00[ASN][1000 genomes]
rs3750236	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3750237	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3793402	0.96[ASN][1000 genomes]
rs3793447	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3860845	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4007685	1.00[ASN][1000 genomes]
rs4347009	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4870932	0.99[ASN][1000 genomes]
rs4870933	0.99[ASN][1000 genomes]
rs6470327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6470328	1.00[ASN][1000 genomes]
rs6651230	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6989560	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[ASN][1000 genomes]
rs7001228	0.90[ASN][1000 genomes]
rs7003069	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7007960	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7008915	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7018283	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7813917	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7825911	0.99[ASN][1000 genomes]
rs7832609	0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9297707	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030748	chr8:126012282-126137840	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv539743	chr8:126012282-126137840	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs966946	FER1L6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126011800-126034000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr8:126013400-126040400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr8:126013400-126042600	Weak transcription	Right Ventricle	heart
4	chr8:126013600-126052200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:126014400-126031400	Strong transcription	NHDF-Ad	bronchial
6	chr8:126014600-126044000	Weak transcription	Stomach Mucosa	stomach
7	chr8:126015400-126036800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr8:126015400-126037400	Strong transcription	A549	lung
9	chr8:126015400-126037600	Strong transcription	HSMM	muscle
10	chr8:126015400-126098000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:126015600-126031400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr8:126015600-126031600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:126015600-126037000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr8:126015600-126039000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:126015600-126041000	Strong transcription	Fetal Thymus	thymus
16	chr8:126015800-126037400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr8:126016000-126041400	Strong transcription	Liver	Liver
18	chr8:126016400-126036800	Strong transcription	K562	blood
19	chr8:126016600-126036400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:126017000-126035400	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:126017200-126036800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:126017600-126032400	Strong transcription	Fetal Muscle Leg	muscle
23	chr8:126017600-126037600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr8:126017800-126036800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr8:126017800-126037400	Strong transcription	HUVEC	blood vessel
26	chr8:126017800-126038400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr8:126018000-126037800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr8:126019200-126031600	Strong transcription	Osteobl	bone
29	chr8:126019600-126071800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:126021200-126041200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr8:126023400-126038400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr8:126023600-126099000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr8:126024000-126037600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr8:126024200-126038000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr8:126024400-126037400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:126024600-126043200	Weak transcription	Fetal Brain Male	brain
37	chr8:126026200-126032000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr8:126026400-126032000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr8:126026400-126037600	Strong transcription	NH-A	brain
40	chr8:126026600-126038600	Strong transcription	Dnd41	blood
41	chr8:126027000-126037400	Strong transcription	Fetal Brain Female	brain
42	chr8:126027000-126037600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr8:126027200-126036600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:126027400-126038000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr8:126027600-126034200	Strong transcription	HSMMtube	muscle
46	chr8:126027600-126037600	Strong transcription	Primary T cells from cord blood	blood
47	chr8:126027600-126038400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr8:126027600-126044400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:126027800-126032200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr8:126027800-126032400	Strong transcription	Brain Inferior Temporal Lobe	brain

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