Variant report

Variant	rs12674439
Chromosome Location	chr7:110708969-110708970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:110707719..110710533-chr7:110715072..110716624,2	K562	blood:
2	chr7:110699046..110701763-chr7:110705311..110708989,4	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10226045	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10233469	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10251869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10257075	0.88[JPT][hapmap]
rs10261004	0.89[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap]
rs10261591	0.86[JPT][hapmap]
rs10262354	0.89[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap]
rs10270683	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1034698	0.86[JPT][hapmap]
rs10487301	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10487302	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10487304	0.86[JPT][hapmap]
rs10953676	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953677	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953678	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953679	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10953682	0.86[JPT][hapmap]
rs10953683	0.86[JPT][hapmap]
rs1121497	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11773752	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11976211	0.89[ASW][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs12532608	0.92[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12668074	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12669471	0.85[JPT][hapmap]
rs12674169	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12674347	0.83[ASW][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12705753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12705754	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17158333	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs2014938	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2041659	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2051797	1.00[CEU][hapmap]
rs2107145	0.90[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs2107146	1.00[ASW][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2107147	0.88[ASW][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2110320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214890	0.86[JPT][hapmap]
rs214892	0.86[JPT][hapmap]
rs214893	0.82[JPT][hapmap]
rs214897	0.86[JPT][hapmap]
rs2189323	0.90[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs2894590	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4727755	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730475	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4730477	0.86[JPT][hapmap]
rs4730478	0.84[GIH][hapmap]
rs4730479	0.90[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs4730481	0.90[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4730482	0.86[JPT][hapmap]
rs6466375	0.86[JPT][hapmap]
rs73418014	0.84[ASN][1000 genomes]
rs73418039	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7455821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757219	0.93[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs7778044	0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7781676	0.81[MEX][hapmap]
rs7781715	0.81[MEX][hapmap]
rs7800862	0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap]
rs7804649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs995147	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531434	chr7:110310931-110839892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3506497	chr7:110484691-111091738	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3506498	chr7:110484750-111091689	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2758129	chr7:110523298-110787849	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2759554	chr7:110523298-110787849	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1031546	chr7:110549137-110978256	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv817555	chr7:110564801-110990927	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1033286	chr7:110588021-110990928	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv539063	chr7:110588021-110990928	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv931978	chr7:110607590-111092490	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1025987	chr7:110609568-111258501	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	esv2830178	chr7:110645431-110778571	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1024477	chr7:110660006-110944477	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv608154	chr7:110688993-110945501	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12674439	COG5	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110690800-110714400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:110705600-110714000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:110707000-110714800	Enhancers	Primary T cells from cord blood	blood
4	chr7:110707400-110711800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:110707600-110717800	Weak transcription	Right Atrium	heart
6	chr7:110708000-110709000	Weak transcription	K562	blood
7	chr7:110708600-110709200	Enhancers	Fetal Heart	heart

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