Variant report

Variant	rs944949
Chromosome Location	chr9:95140613-95140614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95128615..95130359-chr9:95138980..95141028,2	MCF-7	breast:
2	chr9:95138915..95141758-chr9:95143289..95145635,2	K562	blood:
3	chr9:95140461..95141981-chr9:107509705..107511221,2	MCF-7	breast:
4	chr9:95134609..95136461-chr9:95140478..95143032,2	K562	blood:

Variant related genes	Relation type
ENSG00000136783	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10120210	1.00[YRI][hapmap]
rs10125510	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1058726	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs1058751	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs10733744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144933	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152760	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1152761	0.86[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1152762	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175737	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1175923	0.88[EUR][1000 genomes]
rs1175929	0.82[EUR][1000 genomes]
rs1175930	0.88[EUR][1000 genomes]
rs1175931	0.81[CEU][hapmap]
rs11787696	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11789578	0.91[EUR][1000 genomes]
rs11791931	0.87[CEU][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs11792542	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs11793505	0.88[EUR][1000 genomes]
rs11794966	0.84[EUR][1000 genomes]
rs12555097	0.82[EUR][1000 genomes]
rs1536423	1.00[YRI][hapmap]
rs2084289	0.88[EUR][1000 genomes]
rs2295939	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2296665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs230223	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398749	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894058	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap]
rs41280213	0.91[EUR][1000 genomes]
rs41280215	0.91[EUR][1000 genomes]
rs472163	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs4743866	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs4743867	0.88[EUR][1000 genomes]
rs4743868	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs4743871	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4744124	0.88[EUR][1000 genomes]
rs4744125	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs501814	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs556155	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs557066	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs55894730	0.91[EUR][1000 genomes]
rs56374228	0.91[EUR][1000 genomes]
rs6479421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7042199	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895639	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs9409464	0.91[EUR][1000 genomes]
rs9409465	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs9409466	0.81[CEU][hapmap]
rs9409467	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409469	1.00[ASW][hapmap];0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409659	0.91[EUR][1000 genomes]
rs9409660	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409661	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs9409662	0.89[EUR][1000 genomes]
rs9409665	0.93[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409666	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1053205	chr9:95119195-95182612	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs944949	ANKRD19	cis	parietal	SCAN
rs944949	C9orf79	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95128000-95141400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:95128400-95146600	Weak transcription	NHEK	skin
3	chr9:95129400-95141400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:95132200-95141200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:95135200-95149800	Weak transcription	Primary B cells from cord blood	blood
6	chr9:95135600-95148000	Weak transcription	Ovary	ovary
7	chr9:95135800-95141200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:95137600-95141000	Weak transcription	Dnd41	blood
9	chr9:95137800-95143600	Weak transcription	Left Ventricle	heart
10	chr9:95138000-95152400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:95138800-95141200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:95139000-95163200	Weak transcription	Aorta	Aorta
13	chr9:95139200-95141200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:95139600-95142000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:95139600-95142000	Enhancers	Fetal Intestine Large	intestine
16	chr9:95139600-95142200	Enhancers	Fetal Thymus	thymus
17	chr9:95139800-95141000	Weak transcription	Thymus	Thymus
18	chr9:95139800-95142600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr9:95139800-95143000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:95140000-95141000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:95140000-95141200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:95140000-95141200	Weak transcription	NH-A	brain
23	chr9:95140200-95140800	Enhancers	H9 Cell Line	embryonic stem cell
24	chr9:95140200-95140800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr9:95140200-95141400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr9:95140200-95141600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:95140200-95141800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:95140200-95142600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:95140400-95140800	Enhancers	Fetal Heart	heart
30	chr9:95140400-95141200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr9:95140400-95142200	Enhancers	Fetal Intestine Small	intestine
32	chr9:95140400-95142800	Enhancers	Primary T cells from cord blood	blood
33	chr9:95140400-95148000	Weak transcription	Fetal Stomach	stomach
34	chr9:95140600-95141000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:95140600-95141400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:95140600-95144000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:95140600-95145000	Weak transcription	K562	blood
38	chr9:95140600-95145600	Weak transcription	Fetal Lung	lung

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