Variant report

Variant	rs7029570
Chromosome Location	chr9:97682788-97682789
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	NFIC	chr9:97682596-97683925	SK-N-SH	brain:	n/a	n/a
2	MAX	chr9:97681372-97685528	A549	lung:	n/a	n/a
3	RCOR1	chr9:97682648-97686148	IMR90	lung:	n/a	n/a
4	SP1	chr9:97681342-97685519	A549	lung:	n/a	n/a
5	TAF1	chr9:97682599-97683214	SK-N-SH	brain:	n/a	n/a
6	REST	chr9:97682505-97685348	A549	lung:	n/a	chr9:97684506-97684526 chr9:97682757-97682770 chr9:97682800-97682813 chr9:97682940-97682950 chr9:97684641-97684654
7	POLR2A	chr9:97682706-97684912	ProgFib	skin:	n/a	n/a
8	EP300	chr9:97682702-97683151	SK-N-SH_RA	brain:	n/a	chr9:97682882-97682896
9	EP300	chr9:97681350-97683738	A549	lung:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
10	FOSL2	chr9:97681546-97685898	A549	lung:	n/a	n/a
11	YY1	chr9:97682638-97682956	A549	lung:	n/a	n/a
12	EGR1	chr9:97681824-97682891	HCT-116	colon:	n/a	n/a
13	CTCF	chr9:97682700-97682850	AG09319	gingival:	n/a	chr9:97682753-97682761
14	REST	chr9:97682636-97683064	SK-N-SH	brain:	n/a	chr9:97682757-97682770 chr9:97682800-97682813 chr9:97682940-97682950
15	POLR2A	chr9:97682660-97682862	A549	lung:	n/a	n/a
16	RAD21	chr9:97682587-97683277	SK-N-SH_RA	brain:	n/a	n/a
17	SP1	chr9:97681324-97685508	A549	lung:	n/a	n/a
18	BCL3	chr9:97681559-97685224	A549	lung:	n/a	n/a
19	POLR2A	chr9:97682617-97682853	A549	lung:	n/a	n/a
20	JUND	chr9:97682622-97683128	A549	lung:	n/a	n/a
21	GATA3	chr9:97681311-97685467	A549	lung:	n/a	n/a
22	TAF1	chr9:97682484-97683748	A549	lung:	n/a	n/a
23	GATA3	chr9:97682576-97683912	SK-N-SH	brain:	n/a	n/a
24	CEBPB	chr9:97682787-97683173	IMR90	lung:	n/a	n/a
25	EP300	chr9:97682661-97683162	SK-N-SH_RA	brain:	n/a	chr9:97682882-97682896
26	EP300	chr9:97682605-97684015	SK-N-SH	brain:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
27	TCF12	chr9:97681294-97685653	A549	lung:	n/a	chr9:97685588-97685595
28	CEBPB	chr9:97682745-97683201	A549	lung:	n/a	n/a
29	POLR2A	chr9:97682580-97683221	A549	lung:	n/a	n/a
30	RAD21	chr9:97682658-97683072	SK-N-SH_RA	brain:	n/a	n/a
31	SIN3AK20	chr9:97682676-97683733	A549	lung:	n/a	n/a
32	SIX5	chr9:97681767-97685733	A549	lung:	n/a	n/a
33	TEAD4	chr9:97682550-97683768	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr9:97682640-97682980	A549	lung:	n/a	n/a
35	CTCF	chr9:97682740-97682890	AG04449	skin:	n/a	chr9:97682753-97682761
36	BCL3	chr9:97681414-97683736	A549	lung:	n/a	n/a
37	EP300	chr9:97682704-97683865	SK-N-SH	brain:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
38	JUND	chr9:97681585-97682969	MCF-7	breast:	n/a	n/a
39	MAX	chr9:97682526-97683748	A549	lung:	n/a	n/a
40	GATA3	chr9:97682589-97683840	SK-N-SH	brain:	n/a	n/a
41	TCF12	chr9:97682503-97683929	SK-N-SH	brain:	n/a	n/a
42	SIN3AK20	chr9:97682724-97683265	A549	lung:	n/a	n/a
43	JUND	chr9:97682583-97683799	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr9:97682531-97684225	SK-N-SH	brain:	n/a	n/a
45	E2F6	chr9:97682527-97683398	A549	lung:	n/a	chr9:97683289-97683298
46	TCF12	chr9:97682502-97683888	SK-N-SH	brain:	n/a	n/a
47	TEAD4	chr9:97682533-97683881	SK-N-SH	brain:	n/a	n/a
48	PBX3	chr9:97682646-97683881	SK-N-SH	brain:	n/a	n/a
49	FOXA2	chr9:97681553-97682988	A549	lung:	n/a	n/a
50	CTCF	chr9:97682700-97682850	NHDF-neo	bronchial:	n/a	chr9:97682753-97682761

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97679968..97683217-chr9:97810510..97812408,3	MCF-7	breast:
3	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
4	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
5	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
6	chr9:97558473..97564935-chr9:97678907..97687123,11	MCF-7	breast:
7	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000230815	Chromatin interaction
ENSG00000252153	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1004813	0.82[JPT][hapmap]
rs10125566	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10217441	0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs10512252	0.82[JPT][hapmap]
rs10732407	0.84[AMR][1000 genomes]
rs10739988	0.84[AMR][1000 genomes]
rs10739990	0.84[AMR][1000 genomes]
rs10739991	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10761362	0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs10821411	0.84[AMR][1000 genomes]
rs10993435	1.00[CEU][hapmap]
rs10993449	1.00[CEU][hapmap]
rs1113967	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12551506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12552838	1.00[AMR][1000 genomes]
rs12554043	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12555128	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs12682668	0.82[JPT][hapmap]
rs12683896	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12684139	0.82[JPT][hapmap]
rs12684154	0.82[JPT][hapmap]
rs12684461	0.82[JPT][hapmap]
rs12684470	0.82[JPT][hapmap]
rs12686277	0.82[JPT][hapmap]
rs12686500	0.82[JPT][hapmap]
rs1382411	0.88[AMR][1000 genomes]
rs1382412	0.88[AMR][1000 genomes]
rs1530331	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs1542107	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1571897	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs16905557	0.82[JPT][hapmap]
rs16911801	0.82[JPT][hapmap]
rs16911802	0.82[JPT][hapmap]
rs16911817	0.82[JPT][hapmap]
rs16911821	0.82[JPT][hapmap]
rs16911826	0.82[JPT][hapmap]
rs16911834	1.00[AMR][1000 genomes]
rs16911856	0.80[AMR][1000 genomes]
rs1806996	0.82[JPT][hapmap]
rs1904201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2026399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061799	0.81[GIH][hapmap]
rs2078379	0.82[JPT][hapmap]
rs2095069	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2119953	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2165715	1.00[MEX][hapmap]
rs2406897	0.84[AMR][1000 genomes]
rs2406898	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs2584805	0.88[MEX][hapmap]
rs2896816	1.00[CEU][hapmap]
rs2897523	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs356148	0.88[MEX][hapmap]
rs3824493	0.82[JPT][hapmap]
rs3847309	0.82[JPT][hapmap]
rs3847310	0.82[JPT][hapmap]
rs3847311	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3886567	0.82[JPT][hapmap]
rs3886568	0.80[ASW][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3887267	0.88[MEX][hapmap]
rs41316526	0.88[AMR][1000 genomes]
rs4332191	0.84[AMR][1000 genomes]
rs438742	0.88[MEX][hapmap]
rs4743976	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs4744389	0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs6479568	0.82[JPT][hapmap]
rs6479576	0.82[JPT][hapmap]
rs6479578	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs6479581	0.84[AMR][1000 genomes]
rs66642068	0.88[AMR][1000 genomes]
rs66863985	0.88[AMR][1000 genomes]
rs66993340	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67490803	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67756624	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7019602	1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes]
rs7022739	0.81[GIH][hapmap]
rs7022963	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7026714	0.82[JPT][hapmap]
rs7035166	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap]
rs7038519	0.82[JPT][hapmap]
rs7038891	0.88[MEX][hapmap]
rs7042271	1.00[CEU][hapmap]
rs7044371	0.84[AMR][1000 genomes]
rs7045005	0.82[JPT][hapmap]
rs7046900	0.84[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72748601	1.00[AMR][1000 genomes]
rs73538177	0.88[AMR][1000 genomes]
rs7465900	0.82[JPT][hapmap]
rs7850601	0.82[JPT][hapmap]
rs7850680	0.82[JPT][hapmap]
rs7852844	0.85[ASN][1000 genomes]
rs7867856	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7869736	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7870679	0.82[JPT][hapmap]
rs894426	0.84[AMR][1000 genomes]
rs894427	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs894428	0.82[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7029570	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97671000-97684200	Weak transcription	Small Intestine	intestine
5	chr9:97675000-97684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:97675400-97684000	Weak transcription	Psoas Muscle	Psoas
7	chr9:97676600-97683000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97676600-97684200	Weak transcription	Colonic Mucosa	Colon
9	chr9:97676800-97683400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:97677000-97684000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:97677400-97688600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:97678000-97683000	Weak transcription	Fetal Intestine Large	intestine
13	chr9:97678000-97684400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:97679000-97686400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:97679200-97683200	Enhancers	Stomach Mucosa	stomach
16	chr9:97679200-97687200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:97679400-97687000	Enhancers	Fetal Heart	heart
18	chr9:97679600-97682800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:97679600-97682800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:97679800-97684000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:97679800-97684000	Weak transcription	Fetal Intestine Small	intestine
22	chr9:97679800-97684200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:97679800-97684400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:97679800-97684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:97679800-97686200	Weak transcription	Fetal Thymus	thymus
26	chr9:97680000-97683000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:97680000-97684200	Weak transcription	Fetal Brain Male	brain
28	chr9:97680000-97687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:97680200-97688000	Weak transcription	Gastric	stomach
30	chr9:97680400-97685800	Enhancers	Right Ventricle	heart
31	chr9:97680400-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:97680600-97682800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:97680600-97683200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:97680600-97685000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:97680600-97686400	Enhancers	Ovary	ovary
36	chr9:97680600-97700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:97680800-97682800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:97680800-97683000	Weak transcription	Brain Substantia Nigra	brain
39	chr9:97680800-97684600	Weak transcription	GM12878-XiMat	blood
40	chr9:97680800-97685000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:97681000-97684200	Weak transcription	Pancreas	Pancrea
42	chr9:97681400-97682800	Enhancers	HSMMtube	muscle
43	chr9:97681400-97682800	Enhancers	NHDF-Ad	bronchial
44	chr9:97681400-97684000	Enhancers	Hela-S3	cervix
45	chr9:97681400-97686200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:97681400-97686600	Enhancers	Right Atrium	heart
47	chr9:97681600-97682800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:97681600-97682800	Enhancers	HSMM	muscle
49	chr9:97681600-97683000	Enhancers	NH-A	brain
50	chr9:97681600-97683000	Enhancers	NHLF	lung

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