Variant report

Variant	rs1930246
Chromosome Location	chr9:103231440-103231441
allele	G/T
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	ZNF263	chr9:103230808-103231523	HEK293-T-REx	kidney:	n/a	chr9:103230998-103231019

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103225675..103229353-chr9:103229898..103233058,3	K562	blood:
2	chr9:103231014..103233124-chr9:103234996..103237706,5	MCF-7	breast:

Variant related genes	Relation type
TMEFF1	TF binding region
ENSG00000241697	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:139)

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];0.81[MKK][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1041565	0.97[ASN][1000 genomes]
rs10465118	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10465145	0.89[ASN][1000 genomes]
rs10465147	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][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];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10465149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10512270	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10512271	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819773	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs10819774	0.81[CHB][hapmap];0.89[ASN][1000 genomes]
rs10819775	0.89[ASN][1000 genomes]
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];0.94[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10819779	0.98[ASN][1000 genomes]
rs10819781	1.00[ASN][1000 genomes]
rs10819782	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10819785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819786	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10819788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10819789	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]
rs10819790	0.83[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];0.93[YRI][hapmap]
rs10989085	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10989090	0.94[ASN][1000 genomes]
rs10989091	0.97[ASN][1000 genomes]
rs10989092	0.98[ASN][1000 genomes]
rs10989093	0.95[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];0.88[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10989095	0.98[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];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10989099	1.00[ASN][1000 genomes]
rs10989103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10989107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989108	0.97[ASN][1000 genomes]
rs10989111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989112	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989120	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989121	0.89[ASN][1000 genomes]
rs10989123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10989124	0.84[ASN][1000 genomes]
rs10989127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs10989130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10989131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989134	0.83[ASN][1000 genomes]
rs10989135	0.83[ASN][1000 genomes]
rs10989142	0.83[ASN][1000 genomes]
rs10989143	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10989144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10989145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10989146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs10989147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10989150	0.94[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs10989151	0.82[ASN][1000 genomes]
rs10989152	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10989153	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[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];0.84[AMR][1000 genomes];0.91[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];0.82[TSI][hapmap]
rs11793014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12004257	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12005378	0.87[ASN][1000 genomes]
rs12056981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12057047	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12235981	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12236071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12236952	0.97[ASN][1000 genomes]
rs12236970	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12237166	1.00[ASN][1000 genomes]
rs12237481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12238560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1226588	0.82[YRI][hapmap]
rs12682741	1.00[ASN][1000 genomes]
rs12683122	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12683548	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs13286805	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13292589	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1332598	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs16919136	0.97[ASN][1000 genomes]
rs16919174	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs1930237	0.84[ASN][1000 genomes]
rs1930245	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1931140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][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];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[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];0.81[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2183989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2183990	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs2183991	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs2274881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2274882	0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2780959	0.85[YRI][hapmap]
rs34471402	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34816846	0.86[EUR][1000 genomes]
rs56012200	0.83[ASN][1000 genomes]
rs56020062	0.83[ASN][1000 genomes]
rs56050588	0.85[ASN][1000 genomes]
rs56122790	0.89[ASN][1000 genomes]
rs56170030	0.97[ASN][1000 genomes]
rs59565932	0.84[ASN][1000 genomes]
rs59611728	0.96[ASN][1000 genomes]
rs59823190	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7021028	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7024666	1.00[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];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7029001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7031884	0.90[JPT][hapmap];0.89[YRI][hapmap]
rs7034154	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7038306	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7041933	1.00[ASN][1000 genomes]
rs7042669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7046659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs7049241	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72735107	0.89[ASN][1000 genomes]
rs72735110	0.89[ASN][1000 genomes]
rs72735119	0.98[ASN][1000 genomes]
rs72735122	0.98[ASN][1000 genomes]
rs72735140	0.97[ASN][1000 genomes]
rs72735148	0.89[ASN][1000 genomes]
rs7850353	0.85[EUR][1000 genomes]
rs7869933	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1930246	C9orf125	cis	cerebellum	SCAN
rs1930246	C9orf21	cis	cerebellum	SCAN
rs1930246	C9orf30	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103216600-103235000	Weak transcription	Aorta	Aorta
2	chr9:103216800-103235000	Weak transcription	Fetal Muscle Leg	muscle
3	chr9:103217000-103234800	Weak transcription	Fetal Brain Female	brain
4	chr9:103217200-103234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:103218200-103235000	Weak transcription	NHLF	lung
6	chr9:103218400-103235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:103220200-103234800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:103228000-103232800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:103228600-103233000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:103228800-103234600	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:103228800-103235000	Weak transcription	Adipose Nuclei	Adipose
12	chr9:103229000-103235000	Weak transcription	Pancreas	Pancrea
13	chr9:103229400-103235000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:103229600-103234600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:103230000-103234800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:103230200-103234800	Weak transcription	Brain Anterior Caudate	brain
17	chr9:103230200-103235000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:103230400-103231800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:103230400-103234800	Weak transcription	Brain Angular Gyrus	brain
20	chr9:103230600-103234600	Weak transcription	HepG2	liver
21	chr9:103231200-103231600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:103231200-103231600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr9:103231200-103231600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr9:103231200-103231800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:103231200-103231800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:103231200-103232200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:103231200-103232600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr9:103231400-103231800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr9:103231400-103232200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:103231400-103232200	Enhancers	Psoas Muscle	Psoas

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