Variant report

Variant	rs2406898
Chromosome Location	chr9:97634358-97634359
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97632109..97634488-chr9:97681689..97683575,2	MCF-7	breast:
2	chr9:97633916..97636147-chr9:97641921..97644696,2	MCF-7	breast:
3	chr9:97626766..97634519-chr9:97675095..97684236,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1004813	1.00[JPT][hapmap]
rs10125566	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10217441	1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10512252	1.00[JPT][hapmap]
rs10732407	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10739988	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10739989	0.84[AFR][1000 genomes]
rs10739990	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10739991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10761362	1.00[TSI][hapmap];0.97[AMR][1000 genomes]
rs10761363	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821407	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821411	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10993351	0.86[MKK][hapmap]
rs10993386	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1113967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1228614	0.83[YRI][hapmap]
rs12551506	0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs12552838	0.84[AMR][1000 genomes]
rs12554043	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs12555128	1.00[TSI][hapmap]
rs12682668	1.00[JPT][hapmap]
rs12683896	0.84[AMR][1000 genomes]
rs12684072	1.00[JPT][hapmap]
rs12684139	1.00[JPT][hapmap]
rs12684154	1.00[JPT][hapmap]
rs12684461	1.00[JPT][hapmap]
rs12684470	1.00[JPT][hapmap]
rs12684781	1.00[JPT][hapmap]
rs12686277	1.00[JPT][hapmap]
rs12686500	1.00[JPT][hapmap]
rs13285343	0.83[YRI][hapmap]
rs1530331	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1542108	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1571897	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs16905557	1.00[JPT][hapmap]
rs16911801	1.00[JPT][hapmap]
rs16911802	1.00[JPT][hapmap]
rs16911817	1.00[JPT][hapmap]
rs16911820	1.00[JPT][hapmap]
rs16911821	1.00[JPT][hapmap]
rs16911826	1.00[JPT][hapmap]
rs16911834	0.84[AMR][1000 genomes]
rs1806996	1.00[JPT][hapmap]
rs1904201	0.82[JPT][hapmap];0.81[AMR][1000 genomes]
rs2026399	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2061799	0.81[GIH][hapmap]
rs2078379	1.00[JPT][hapmap]
rs2095069	0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs2119953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2165715	0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2406897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242259	0.83[YRI][hapmap]
rs2584803	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs2584805	0.85[TSI][hapmap]
rs2767403	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs2897523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs356122	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs356124	0.83[YRI][hapmap]
rs356127	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs356130	0.86[MKK][hapmap];0.83[YRI][hapmap]
rs356134	0.83[YRI][hapmap]
rs356137	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs356143	0.91[MKK][hapmap];0.83[YRI][hapmap]
rs356146	0.83[YRI][hapmap]
rs356148	0.85[TSI][hapmap]
rs380205	0.89[MKK][hapmap];0.83[YRI][hapmap]
rs3824493	1.00[JPT][hapmap]
rs3847309	1.00[JPT][hapmap]
rs3847310	1.00[JPT][hapmap]
rs3847311	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3886567	1.00[JPT][hapmap]
rs3886568	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3887267	0.85[TSI][hapmap]
rs3910730	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs418764	0.83[YRI][hapmap]
rs4332191	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs438742	0.85[TSI][hapmap]
rs439052	0.83[YRI][hapmap]
rs456276	0.85[TSI][hapmap]
rs4743972	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743973	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4743976	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs4744377	0.83[YRI][hapmap]
rs4744387	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744402	0.86[AMR][1000 genomes]
rs6479568	1.00[JPT][hapmap]
rs6479576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479578	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479579	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479581	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479582	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479583	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6479589	1.00[CEU][hapmap]
rs66993340	0.81[AMR][1000 genomes]
rs67490803	0.84[AMR][1000 genomes]
rs7019602	0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7022739	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs7022963	1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7025100	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7025934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7026714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029570	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]
rs7030703	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7031637	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7035166	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038891	0.85[TSI][hapmap]
rs7044371	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7045005	1.00[JPT][hapmap]
rs7046900	0.84[AMR][1000 genomes]
rs72748601	0.84[AMR][1000 genomes]
rs7465900	1.00[JPT][hapmap]
rs7850601	1.00[JPT][hapmap]
rs7850680	1.00[JPT][hapmap]
rs7852844	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7861358	0.83[YRI][hapmap]
rs7864389	0.89[AMR][1000 genomes]
rs7867856	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7869736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7870679	1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894426	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs894427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs894428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2406898	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97625000-97637800	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97626000-97638200	Enhancers	HSMM	muscle
3	chr9:97626000-97638400	Enhancers	HSMMtube	muscle
4	chr9:97627200-97638000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:97627400-97637800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:97628600-97641000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:97629200-97634600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:97629200-97635800	Enhancers	HMEC	breast
9	chr9:97629200-97636000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:97629600-97635200	Enhancers	Placenta	Placenta
11	chr9:97630000-97638400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:97630000-97645000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:97630200-97634400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:97630200-97636800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:97630200-97637600	Enhancers	Osteobl	bone
16	chr9:97630200-97638000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:97630200-97638200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:97630200-97638200	Enhancers	NHDF-Ad	bronchial
19	chr9:97630200-97640800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr9:97630600-97636800	Enhancers	Fetal Heart	heart
21	chr9:97630600-97637800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:97630600-97643600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:97630800-97635000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:97630800-97637000	Weak transcription	Fetal Intestine Large	intestine
25	chr9:97630800-97644200	Weak transcription	Adipose Nuclei	Adipose
26	chr9:97631000-97634400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr9:97631000-97635000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:97631000-97635400	Weak transcription	Fetal Intestine Small	intestine
29	chr9:97631000-97637000	Weak transcription	Brain Substantia Nigra	brain
30	chr9:97631000-97637200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:97631000-97637600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:97631000-97637800	Weak transcription	Aorta	Aorta
33	chr9:97631000-97640000	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:97631200-97634800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:97631600-97634600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:97631600-97635200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:97631800-97634600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr9:97631800-97634800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr9:97631800-97635000	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:97631800-97637800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:97631800-97645600	Weak transcription	Small Intestine	intestine
42	chr9:97632000-97634600	Weak transcription	Ovary	ovary
43	chr9:97632000-97635000	Weak transcription	Fetal Lung	lung
44	chr9:97632000-97637600	Weak transcription	Liver	Liver
45	chr9:97632000-97640600	Weak transcription	K562	blood
46	chr9:97632000-97646000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:97632200-97634400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr9:97632200-97634600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr9:97632400-97634400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr9:97632800-97634400	Flanking Active TSS	Hela-S3	cervix

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