Variant report

Variant	rs10819789
Chromosome Location	chr9:103287685-103287686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103286667..103289136-chr9:103299803..103302650,2	MCF-7	breast:
2	chr9:103274017..103275982-chr9:103287555..103289567,2	K562	blood:
3	chr9:103281981..103284118-chr9:103285879..103288033,2	MCF-7	breast:
4	chr9:103282396..103285475-chr9:103285908..103289146,4	K562	blood:
5	chr9:103286876..103289337-chr9:103312993..103315627,2	K562	blood:
6	chr9:103100588..103103062-chr9:103287434..103290321,2	K562	blood:

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1000477	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];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1041565	0.87[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10465119	0.90[ASN][1000 genomes]
rs10465147	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10465148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10465149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10512271	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10819773	1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10819774	0.81[CHB][hapmap]
rs10819776	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs10819779	0.82[ASN][1000 genomes]
rs10819781	0.84[ASN][1000 genomes]
rs10819782	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs10819785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819786	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10819788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10819790	0.99[ASN][1000 genomes]
rs10989078	1.00[JPT][hapmap]
rs10989081	1.00[JPT][hapmap]
rs10989082	0.94[ASW][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10989085	1.00[JPT][hapmap]
rs10989091	0.81[ASN][1000 genomes]
rs10989092	0.82[ASN][1000 genomes]
rs10989094	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs10989095	0.82[ASN][1000 genomes]
rs10989097	0.94[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs10989099	0.84[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989108	0.87[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989124	1.00[ASN][1000 genomes]
rs10989127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10989130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989134	0.99[ASN][1000 genomes]
rs10989135	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10989140	0.87[ASN][1000 genomes]
rs10989142	0.99[ASN][1000 genomes]
rs10989143	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10989146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10989150	0.94[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989151	0.98[ASN][1000 genomes]
rs10989152	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][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];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10989154	0.94[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs10989156	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][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];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12004257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12057047	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12235981	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12236952	0.87[ASN][1000 genomes]
rs12236970	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12237166	0.84[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1226588	0.85[YRI][hapmap]
rs1226594	0.82[YRI][hapmap]
rs12682741	0.84[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[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];0.84[ASN][1000 genomes]
rs13286805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13292589	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1332598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16919136	0.87[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs1930237	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1930245	0.84[ASN][1000 genomes]
rs1930246	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];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1931140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2026423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069236	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]
rs2151106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2183989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2183990	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2183991	0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2274882	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2780959	0.89[YRI][hapmap]
rs34471402	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34816846	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55827987	0.82[ASN][1000 genomes]
rs56163523	0.82[ASN][1000 genomes]
rs56170030	0.87[ASN][1000 genomes]
rs59565932	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59611728	0.86[ASN][1000 genomes]
rs59823190	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][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];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7024666	0.84[ASN][1000 genomes]
rs7028822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7029001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031884	0.90[JPT][hapmap];0.85[YRI][hapmap]
rs7034154	0.84[ASN][1000 genomes]
rs7038306	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7041933	0.84[ASN][1000 genomes]
rs7042669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7046659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs7049241	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72735119	0.82[ASN][1000 genomes]
rs72735122	0.82[ASN][1000 genomes]
rs72735140	0.87[ASN][1000 genomes]
rs72735154	0.90[ASN][1000 genomes]
rs7850353	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7869933	0.84[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10819789	C9orf125	cis	cerebellum	SCAN
rs10819789	C9orf21	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103255600-103301600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:103257000-103289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:103258600-103296400	Weak transcription	Brain Anterior Caudate	brain
4	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
5	chr9:103263200-103312200	Weak transcription	Fetal Kidney	kidney
6	chr9:103263400-103327600	Weak transcription	Aorta	Aorta
7	chr9:103270000-103289200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:103270800-103290000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:103272600-103307000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:103273000-103303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:103273400-103289400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
13	chr9:103274400-103289400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:103278000-103287800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:103278200-103289600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:103278400-103288200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr9:103278400-103306400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:103278400-103333000	Weak transcription	Fetal Brain Male	brain
19	chr9:103278800-103288000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:103279600-103312000	Weak transcription	HSMM	muscle
21	chr9:103280800-103296200	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:103283400-103296400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:103284400-103296400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:103286400-103288000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:103286600-103288000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:103286600-103290400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:103286800-103289800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr9:103287000-103288600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:103287000-103289200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:103287000-103289400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:103287200-103288000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:103287200-103288000	Strong transcription	Brain Germinal Matrix	brain
33	chr9:103287600-103287800	Enhancers	Psoas Muscle	Psoas
34	chr9:103287600-103288400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:103287600-103289400	Weak transcription	Fetal Brain Female	brain
36	chr9:103287600-103290400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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