Variant report

Variant	rs1110627
Chromosome Location	chr19:39994711-39994712
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39925085..39928337-chr19:39992062..39995488,6	K562	blood:
2	chr19:39992886..39995682-chr19:39996281..39999154,5	K562	blood:
3	chr19:39988896..39990502-chr19:39993866..39995891,2	MCF-7	breast:
4	chr19:39993528..39996626-chr19:40010694..40012599,3	K562	blood:
5	chr19:39897297..39899579-chr19:39992727..39996062,3	K562	blood:
6	chr19:39993663..39995682-chr19:39996281..39998082,2	K562	blood:
7	chr19:39969549..39972807-chr19:39992061..39995133,4	K562	blood:

Variant related genes	Relation type
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10412931	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423537	0.90[EUR][1000 genomes]
rs10424217	0.83[EUR][1000 genomes]
rs1130180	0.86[EUR][1000 genomes]
rs12609112	0.86[EUR][1000 genomes]
rs12978920	0.83[EUR][1000 genomes]
rs12983040	0.86[EUR][1000 genomes]
rs1529732	0.86[EUR][1000 genomes]
rs1560730	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs1865091	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1865092	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs1932	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs2009970	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs2060270	0.87[EUR][1000 genomes]
rs2060271	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2060272	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2116932	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs2288933	0.93[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs2288934	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2304219	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2304221	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2353678	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2353679	0.80[EUR][1000 genomes]
rs251855	0.89[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs251857	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs251858	0.81[EUR][1000 genomes]
rs251859	0.89[CEU][hapmap]
rs28528765	0.87[EUR][1000 genomes]
rs28649498	0.86[EUR][1000 genomes]
rs31727	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs31728	0.92[CEU][hapmap]
rs34918990	0.90[EUR][1000 genomes]
rs35647910	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4390710	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4802026	0.83[EUR][1000 genomes]
rs4803237	0.86[EUR][1000 genomes]
rs4803240	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4803241	0.85[EUR][1000 genomes]
rs4803242	0.86[EUR][1000 genomes]
rs4803245	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803246	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803247	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803250	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs564577	0.89[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs566130	0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs59007555	0.86[EUR][1000 genomes]
rs6508862	0.85[EUR][1000 genomes]
rs6508863	0.85[EUR][1000 genomes]
rs6508864	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6508865	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs686956	0.80[EUR][1000 genomes]
rs7251384	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7251652	0.88[EUR][1000 genomes]
rs7255253	0.86[EUR][1000 genomes]
rs7257526	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73035416	0.87[EUR][1000 genomes]
rs73549933	0.87[EUR][1000 genomes]
rs8107194	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs8107647	0.87[EUR][1000 genomes]
rs8110134	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs8110716	0.85[EUR][1000 genomes]
rs8111260	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs878754	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1110627	GRIK5	cis	parietal	SCAN
rs1110627	NUMBL	cis	parietal	SCAN
rs1110627	RPS16	Cis_1M	lymphoblastoid	RTeQTL
rs1110627	BCAM	cis	parietal	SCAN
rs1110627	RPS16	cis	lymphoblastoid	seeQTL
rs1110627	B3GNT8	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39989400-39997600	Weak transcription	Right Atrium	heart
2	chr19:39990200-39997600	Weak transcription	Gastric	stomach
3	chr19:39991400-39996400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:39993600-39995000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39994000-39996400	Strong transcription	Brain Germinal Matrix	brain
6	chr19:39994000-39997200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:39994000-39997400	Weak transcription	Fetal Brain Male	brain
8	chr19:39994000-39997600	Weak transcription	Pancreas	Pancrea
9	chr19:39994200-39995800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:39994200-39995800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:39994200-39997200	Weak transcription	K562	blood
12	chr19:39994400-39995200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:39994400-39996000	Strong transcription	Fetal Brain Female	brain
14	chr19:39994600-39994800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

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