Variant report

Variant	rs1394
Chromosome Location	chr8:9511654-9511655
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	chr8:9411683..9414392-chr8:9510585..9512196,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173273	Chromatin interaction
ENSG00000272267	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10092751	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10094989	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10099122	0.84[ASN][1000 genomes]
rs10102170	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs10109026	0.86[JPT][hapmap]
rs10111376	0.82[YRI][hapmap]
rs11249934	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs11776236	0.82[YRI][hapmap]
rs11778555	0.82[EUR][1000 genomes]
rs11782886	0.82[EUR][1000 genomes]
rs11785458	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11785923	0.82[EUR][1000 genomes]
rs12114661	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12155819	0.89[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12541617	0.87[YRI][hapmap]
rs12542457	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12542912	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12543959	0.89[YRI][hapmap]
rs12544371	0.85[YRI][hapmap]
rs12545250	0.86[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12547642	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12677313	0.82[YRI][hapmap]
rs12677507	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12679180	0.82[YRI][hapmap]
rs12679956	0.81[EUR][1000 genomes]
rs12682175	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13250951	0.82[YRI][hapmap]
rs13260526	0.82[YRI][hapmap]
rs13263409	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs13264850	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13270518	0.96[YRI][hapmap]
rs13272424	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13276086	0.86[CEU][hapmap];0.98[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs33994795	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35316422	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4075359	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4128198	0.86[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4129360	0.95[CEU][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4422774	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4554469	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4612345	0.82[EUR][1000 genomes]
rs4840426	0.89[ASW][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap]
rs4840437	0.89[ASW][hapmap];0.82[GIH][hapmap];0.82[LWK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap]
rs4841196	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4841203	0.80[EUR][1000 genomes]
rs4841204	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6601327	0.81[ASW][hapmap];0.83[YRI][hapmap]
rs6601338	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6601340	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6601350	0.81[EUR][1000 genomes]
rs67711814	0.84[EUR][1000 genomes]
rs6982148	0.95[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes]
rs6990300	0.94[ASW][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap]
rs6990418	0.86[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6992666	0.81[EUR][1000 genomes]
rs6994574	0.95[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7003791	0.87[YRI][hapmap]
rs7004937	0.86[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7006985	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73202879	0.85[ASN][1000 genomes]
rs7461939	0.95[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7462070	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7822700	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs7835002	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7840706	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7846399	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9644704	0.83[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9644707	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9650639	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1394	MFHAS1	cis	cerebellum	SCAN
rs1394	PPP1R3B	cis	lymphoblastoid	seeQTL
rs1394	TNKS	cis	parietal	SCAN
rs1394	DEFB134	cis	cerebellum	SCAN
rs1394	FLJ10661	cis	cerebellum	SCAN
rs1394	CTSB	cis	cerebellum	SCAN
rs1394	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9495800-9531000	Weak transcription	Gastric	stomach
2	chr8:9499800-9512400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr8:9501600-9525400	Weak transcription	Thymus	Thymus
4	chr8:9501800-9528400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:9501800-9534400	Weak transcription	Fetal Heart	heart
6	chr8:9503000-9521200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr8:9504200-9529400	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:9504400-9512200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr8:9504800-9549600	Weak transcription	Pancreas	Pancrea
10	chr8:9506000-9521200	Weak transcription	Aorta	Aorta
11	chr8:9506400-9530200	Weak transcription	HepG2	liver
12	chr8:9507800-9529400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr8:9508000-9512600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr8:9508200-9512200	Weak transcription	Fetal Thymus	thymus
15	chr8:9508400-9521200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr8:9509000-9513200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr8:9509000-9513400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:9509000-9514000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:9509200-9512200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:9509200-9512400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr8:9509200-9522400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr8:9509400-9512200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:9509400-9512200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:9509400-9512400	Weak transcription	Adipose Nuclei	Adipose
25	chr8:9509400-9512400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr8:9509400-9512600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:9509400-9512800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:9509400-9513400	Weak transcription	HSMMtube	muscle
29	chr8:9509400-9513600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:9509400-9516000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:9509400-9523000	Weak transcription	Brain Anterior Caudate	brain
32	chr8:9509400-9545000	Weak transcription	HSMM	muscle
33	chr8:9509600-9513600	Weak transcription	HMEC	breast
34	chr8:9509600-9529400	Weak transcription	Spleen	Spleen
35	chr8:9509600-9532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr8:9509800-9512400	Weak transcription	Lung	lung
37	chr8:9510000-9528800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr8:9510200-9512600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr8:9510400-9511800	Enhancers	Primary B cells from peripheral blood	blood
40	chr8:9510400-9511800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:9510400-9511800	ZNF genes & repeats	GM12878-XiMat	blood
42	chr8:9510400-9512400	ZNF genes & repeats	Dnd41	blood
43	chr8:9510400-9512600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:9510400-9513000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr8:9510400-9513000	Weak transcription	Fetal Brain Male	brain
46	chr8:9510400-9513200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
47	chr8:9510400-9513200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
48	chr8:9510400-9563800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr8:9510600-9512200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:9510600-9512400	ZNF genes & repeats	Primary T cells from cord blood	blood

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