Variant report

Variant	rs12684438
Chromosome Location	chr9:103170524-103170525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:103168940..103170957-chr9:103175150..103176898,2	K562	blood:
2	chr9:103169457..103171341-chr9:103175056..103176650,2	K562	blood:
3	chr9:103169516..103171661-chr9:103172507..103175663,3	MCF-7	breast:
4	chr9:103170121..103172930-chr9:103214537..103217403,2	K562	blood:
5	chr9:103169067..103171362-chr9:103188981..103190855,2	MCF-7	breast:
6	chr9:103169067..103171157-chr9:103188584..103190825,2	K562	blood:
7	chr9:103169657..103172715-chr9:103188137..103190084,3	K562	blood:
8	chr9:103169579..103171733-chr9:103173238..103174816,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1000477	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10465118	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10465147	1.00[JPT][hapmap]
rs10465148	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10465149	1.00[JPT][hapmap]
rs10512270	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10512271	1.00[JPT][hapmap]
rs10819770	0.86[CHB][hapmap]
rs10819773	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819774	0.93[CHB][hapmap];0.80[EUR][1000 genomes]
rs10819776	0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10819782	1.00[JPT][hapmap]
rs10819785	1.00[JPT][hapmap]
rs10819787	1.00[JPT][hapmap]
rs10819788	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10819789	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs10989078	0.85[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs10989081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10989082	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10989085	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10989094	0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10989097	0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10989103	1.00[JPT][hapmap]
rs10989105	1.00[JPT][hapmap]
rs10989107	1.00[JPT][hapmap]
rs10989111	1.00[JPT][hapmap]
rs10989112	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10989113	1.00[JPT][hapmap]
rs10989114	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10989115	1.00[JPT][hapmap]
rs10989120	0.90[CHD][hapmap];0.81[JPT][hapmap]
rs10989123	1.00[JPT][hapmap]
rs10989127	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10989130	1.00[JPT][hapmap]
rs10989131	1.00[JPT][hapmap]
rs10989144	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10989145	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10989146	1.00[JPT][hapmap]
rs10989147	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10989150	0.82[JPT][hapmap]
rs10989153	0.84[CHD][hapmap]
rs10989154	0.81[CHD][hapmap]
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	0.82[JPT][hapmap]
rs11793014	1.00[JPT][hapmap]
rs12004257	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12056981	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12236071	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12236970	0.84[CHD][hapmap]
rs12237481	1.00[JPT][hapmap]
rs12238560	1.00[JPT][hapmap]
rs12683122	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12683548	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12683889	0.82[JPT][hapmap]
rs12684454	1.00[JPT][hapmap]
rs1332598	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs16919174	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs16919204	0.81[JPT][hapmap]
rs16919211	0.82[JPT][hapmap]
rs1930246	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2026423	0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2069236	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2151106	1.00[JPT][hapmap]
rs2183989	1.00[JPT][hapmap]
rs2183990	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2183991	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2274881	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2274882	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7021028	0.81[CHD][hapmap]
rs7028822	0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7029001	1.00[JPT][hapmap]
rs7031884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7042669	1.00[JPT][hapmap]
rs7046596	0.98[ASN][1000 genomes]
rs7046659	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs72733399	1.00[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12684438	C9orf30	Cis_1M	lymphoblastoid	RTeQTL
rs12684438	CA11	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103169400-103173600	Weak transcription	Right Atrium	heart
2	chr9:103169800-103173600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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