Variant report

Variant	rs2069236
Chromosome Location	chr9:103259790-103259791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103257613..103260503-chr9:103266452..103268152,2	MCF-7	breast:
2	chr9:103196615..103198687-chr9:103259403..103260932,2	MCF-7	breast:
3	chr9:103258953..103260847-chr9:103265590..103267200,2	K562	blood:

Extended variants
information (count: 128 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1000477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1041565	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10465119	0.87[ASN][1000 genomes]
rs10465147	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10465148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10465149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10512271	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10819773	1.00[JPT][hapmap]
rs10819774	0.81[CHB][hapmap]
rs10819776	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10819779	0.86[ASN][1000 genomes]
rs10819781	0.88[ASN][1000 genomes]
rs10819782	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10819785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819786	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819788	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10819789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	1.00[JPT][hapmap]
rs10989082	0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10989085	1.00[JPT][hapmap]
rs10989090	0.85[ASN][1000 genomes]
rs10989091	0.87[ASN][1000 genomes]
rs10989092	0.86[ASN][1000 genomes]
rs10989093	0.83[ASN][1000 genomes]
rs10989094	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[ASN][1000 genomes]
rs10989095	0.86[ASN][1000 genomes]
rs10989097	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.88[ASN][1000 genomes]
rs10989099	0.88[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989104	0.88[ASN][1000 genomes]
rs10989105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989108	0.89[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10989121	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10989123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10989127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10989130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10989135	0.80[AMR][1000 genomes]
rs10989140	0.84[ASN][1000 genomes]
rs10989143	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10989146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989150	0.94[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10989152	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10989153	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10989154	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs10989156	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10989161	0.82[JPT][hapmap]
rs10989162	0.82[JPT][hapmap]
rs10989163	0.82[JPT][hapmap]
rs10989164	0.82[JPT][hapmap]
rs10989165	0.82[JPT][hapmap]
rs10989167	0.82[JPT][hapmap]
rs10989169	0.82[JPT][hapmap]
rs10989170	0.80[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs11793014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12004257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12057047	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12235981	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12236952	0.89[ASN][1000 genomes]
rs12236970	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12237166	0.88[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12682741	0.88[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12683889	0.82[JPT][hapmap]
rs12684438	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs12684454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13286805	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13292589	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1332598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16919136	0.89[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs1930245	0.88[ASN][1000 genomes]
rs1930246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1931140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2026423	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2151106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2183989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2183990	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2183991	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2274882	0.80[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs34471402	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34816846	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56170030	0.89[ASN][1000 genomes]
rs59565932	0.80[AMR][1000 genomes]
rs59611728	0.88[ASN][1000 genomes]
rs59823190	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7021028	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7024666	0.88[ASN][1000 genomes]
rs7028822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7029001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7031884	0.90[JPT][hapmap]
rs7034154	0.88[ASN][1000 genomes]
rs7038306	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7041933	0.88[ASN][1000 genomes]
rs7042669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7046659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7049241	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72735119	0.86[ASN][1000 genomes]
rs72735122	0.86[ASN][1000 genomes]
rs72735140	0.89[ASN][1000 genomes]
rs72735148	0.99[ASN][1000 genomes]
rs72735154	0.87[ASN][1000 genomes]
rs7850353	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7869933	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2069236	C9orf21	cis	cerebellum	SCAN
rs2069236	C9orf125	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103238200-103264200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:103238200-103274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:103255200-103261000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr9:103255200-103271000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:103255400-103277600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:103255600-103265800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:103255600-103266000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:103255600-103272400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:103255600-103272400	Weak transcription	Fetal Brain Female	brain
10	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:103255800-103259800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:103255800-103259800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:103255800-103266000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:103255800-103272400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:103256000-103259800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:103256200-103265000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:103256200-103287400	Weak transcription	HSMMtube	muscle
18	chr9:103256400-103271600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:103257000-103259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:103257000-103272400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:103257200-103260800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:103257200-103261000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:103258000-103261000	Enhancers	Brain Angular Gyrus	brain
25	chr9:103258200-103263600	Weak transcription	Brain Germinal Matrix	brain
26	chr9:103258600-103259800	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
28	chr9:103259000-103260400	Enhancers	Brain Substantia Nigra	brain
29	chr9:103259200-103260400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:103259400-103260800	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:103259400-103261600	Enhancers	HUES48 Cell Line	embryonic stem cell

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