Variant report

Variant	rs7853904
Chromosome Location	chr9:101550367-101550368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:101550275-101550453	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:101548936-101551202	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:101545059..101549166-chr9:101549298..101553118,4	MCF-7	breast:
2	chr9:101550225..101553756-chr9:101569289..101571539,3	MCF-7	breast:
3	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000165138	Chromatin interaction
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10121153	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1022796	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739690	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10760475	0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10760479	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10760494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10819266	0.81[ASN][1000 genomes]
rs10819308	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10819320	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987747	0.88[ASW][hapmap];0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs10987749	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10987771	0.84[EUR][1000 genomes]
rs11791440	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12056975	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs1543506	0.87[ASW][hapmap];0.87[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1555519	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2146255	0.84[EUR][1000 genomes]
rs33998698	0.84[EUR][1000 genomes]
rs3933477	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742737	0.86[ASN][1000 genomes]
rs4742738	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4742741	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4742745	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743278	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743281	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743282	0.85[ASN][1000 genomes]
rs6478839	0.84[ASN][1000 genomes]
rs6478845	0.83[ASN][1000 genomes]
rs7018907	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7020056	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027405	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7027771	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7038640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047722	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7357783	0.85[ASN][1000 genomes]
rs7469116	0.88[ASN][1000 genomes]
rs7861186	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7865233	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9886821	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7853904	C9orf130	cis	cerebellum	SCAN
rs7853904	ZNF189	cis	cerebellum	SCAN
rs7853904	ANKS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
2	chr9:101506800-101553400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:101514400-101553400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
6	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
7	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:101533800-101553200	Strong transcription	Fetal Stomach	stomach
9	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
10	chr9:101535600-101553400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:101535800-101552000	Weak transcription	Thymus	Thymus
12	chr9:101535800-101553400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:101536000-101553200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
16	chr9:101536200-101553400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
18	chr9:101536800-101551400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:101536800-101551600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:101538200-101553000	Weak transcription	NH-A	brain
22	chr9:101538800-101552400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:101539000-101553000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:101541600-101553000	Weak transcription	Brain Anterior Caudate	brain
25	chr9:101542000-101553200	Weak transcription	HUVEC	blood vessel
26	chr9:101542600-101553200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:101544200-101552200	Weak transcription	Spleen	Spleen
28	chr9:101544200-101557600	Weak transcription	Colonic Mucosa	Colon
29	chr9:101544600-101550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:101544600-101551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:101544800-101550400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr9:101544800-101550800	Weak transcription	Fetal Lung	lung
33	chr9:101544800-101551600	Weak transcription	HepG2	liver
34	chr9:101544800-101552000	Weak transcription	Right Ventricle	heart
35	chr9:101544800-101557600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:101545000-101550400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:101545000-101550800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:101545200-101553000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:101545200-101557200	Weak transcription	Liver	Liver
40	chr9:101545400-101553200	Weak transcription	Brain Substantia Nigra	brain
41	chr9:101545800-101550800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:101545800-101553000	Weak transcription	Hela-S3	cervix
43	chr9:101546200-101553000	Weak transcription	Osteobl	bone
44	chr9:101546200-101557600	Weak transcription	Left Ventricle	heart
45	chr9:101546400-101552000	Weak transcription	Fetal Kidney	kidney
46	chr9:101546400-101557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:101546600-101550400	Weak transcription	NHLF	lung
48	chr9:101546600-101550800	Weak transcription	Brain Angular Gyrus	brain
49	chr9:101546600-101551000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:101546600-101551400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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