Variant report

Variant	rs1412488
Chromosome Location	chr9:97780363-97780364
allele	C/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	chr9:97780299-97781609	U87	brain:	n/a	n/a
2	GATA3	chr9:97779666-97781556	A549	lung:	n/a	n/a
3	STAT3	chr9:97780301-97781741	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780
4	MAX	chr9:97780217-97781187	A549	lung:	n/a	chr9:97780770-97780779
5	MAX	chr9:97779614-97781640	A549	lung:	n/a	chr9:97780770-97780779
6	EP300	chr9:97779856-97781372	A549	lung:	n/a	chr9:97781013-97781029 chr9:97780770-97780779
7	FOSL2	chr9:97779833-97781484	A549	lung:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
8	FOS	chr9:97779997-97781508	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780769-97780780
9	POLR2A	chr9:97779974-97781323	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr9:97779653-97781934	MCF10A-Er-Src	breast:	n/a	n/a
11	BCL3	chr9:97779294-97781595	A549	lung:	n/a	chr9:97780770-97780779
12	POLR2A	chr9:97773622-97782824	A549	lung:	n/a	n/a
13	RAD21	chr9:97780149-97781453	IMR90	lung:	n/a	n/a
14	BCL3	chr9:97779555-97780384	A549	lung:	n/a	n/a
15	FOSL2	chr9:97780354-97781354	SK-N-SH	brain:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
16	JUND	chr9:97779801-97781319	SK-N-SH	brain:	n/a	chr9:97780771-97780780 chr9:97780769-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780
17	POLR2A	chr9:97778946-97782848	IMR90	lung:	n/a	n/a
18	POLR2A	chr9:97779495-97781336	MCF10A-Er-Src	breast:	n/a	n/a
19	SP1	chr9:97780282-97781387	A549	lung:	n/a	n/a
20	POLR2A	chr9:97779382-97780575	HepG2	liver:	n/a	n/a
21	FOS	chr9:97779947-97781348	MCF10A-Er-Src	breast:	n/a	chr9:97780771-97780780 chr9:97780844-97780852 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780770-97780780 chr9:97780769-97780780

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97771036..97773650-chr9:97778187..97780629,2	K562	blood:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004373	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10117370	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10119512	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10121760	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10123819	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1020963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512253	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10761364	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761366	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10761368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761369	0.84[EUR][1000 genomes]
rs10761372	0.95[ASN][1000 genomes]
rs10821433	0.89[JPT][hapmap]
rs10993427	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10993456	0.90[JPT][hapmap]
rs10993464	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993467	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1113102	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339639	0.90[JPT][hapmap]
rs12346261	0.90[JPT][hapmap]
rs1564234	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1571894	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1571895	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2061800	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2404302	0.90[CEU][hapmap];0.94[CHB][hapmap]
rs2404305	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2404456	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs3802454	0.90[CEU][hapmap];0.94[CHB][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3802456	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4537362	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743979	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743980	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743981	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743982	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743984	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744423	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744424	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744425	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744426	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744428	0.84[AMR][1000 genomes]
rs4744430	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744431	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744432	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744433	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4744435	0.80[EUR][1000 genomes]
rs4744436	0.81[CEU][hapmap]
rs6479588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479591	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6479592	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7021351	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7022452	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7023719	0.81[CHB][hapmap]
rs7043705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7048786	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7048941	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7851173	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7862156	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7863291	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7865144	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871218	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7873479	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873567	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs962229	0.82[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1412488	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL
rs1412488	FOXE1	cis	parietal	SCAN
rs1412488	OGN	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97768000-97781000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97768000-97781000	Weak transcription	Gastric	stomach
3	chr9:97768000-97783800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:97768000-97786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:97768800-97781800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97768800-97785600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97769000-97783800	Weak transcription	Fetal Brain Male	brain
8	chr9:97769000-97787600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:97769600-97784200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:97770000-97781200	Weak transcription	Small Intestine	intestine
12	chr9:97770600-97780800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:97770800-97781600	Weak transcription	Colonic Mucosa	Colon
14	chr9:97770800-97782000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:97770800-97782200	Weak transcription	Lung	lung
16	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
17	chr9:97771000-97780800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:97771000-97781600	Weak transcription	Primary B cells from cord blood	blood
19	chr9:97772000-97782200	Weak transcription	Esophagus	oesophagus
20	chr9:97772800-97780800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:97772800-97780800	Weak transcription	Right Atrium	heart
22	chr9:97773000-97782200	Weak transcription	Spleen	Spleen
23	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
24	chr9:97774800-97780400	Weak transcription	Hela-S3	cervix
25	chr9:97775200-97780600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:97776000-97780600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:97776000-97781000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:97776000-97784400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr9:97776000-97784600	Strong transcription	Placenta	Placenta
30	chr9:97776400-97785400	Strong transcription	Fetal Intestine Large	intestine
31	chr9:97776600-97780600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:97776800-97780800	Strong transcription	Adipose Nuclei	Adipose
33	chr9:97777000-97780600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:97777200-97782200	Weak transcription	Stomach Mucosa	stomach
35	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
36	chr9:97777600-97780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:97777600-97781000	Weak transcription	Psoas Muscle	Psoas
38	chr9:97778400-97780800	Weak transcription	Right Ventricle	heart
39	chr9:97778600-97780600	Genic enhancers	Colon Smooth Muscle	Colon
40	chr9:97778800-97780800	Weak transcription	Pancreas	Pancrea
41	chr9:97778800-97780800	Genic enhancers	NHDF-Ad	bronchial
42	chr9:97778800-97781000	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr9:97778800-97781000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr9:97778800-97786200	Genic enhancers	Osteobl	bone
45	chr9:97779000-97782800	Genic enhancers	HSMMtube	muscle
46	chr9:97779200-97780600	Weak transcription	Ovary	ovary
47	chr9:97779200-97781000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:97779200-97782200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:97779200-97782200	Weak transcription	Fetal Intestine Small	intestine
50	chr9:97779200-97782400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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