Variant report

Variant	rs8109103
Chromosome Location	chr19:37994111-37994112
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	chr19:37992616..37995600-chr19:37995736..37998672,5	MCF-7	breast:
2	chr19:37991013..37994559-chr19:37994828..37997998,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188227	Chromatin interaction
ENSG00000267115	Chromatin interaction
ENSG00000266916	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10419281	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10425719	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11083423	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666708	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12462546	0.91[ASN][1000 genomes]
rs12981359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17305823	0.82[ASW][hapmap]
rs185368	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs185369	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs1968251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291001	1.00[ASW][hapmap]
rs2306201	1.00[ASW][hapmap]
rs2385180	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385181	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2431992	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs256733	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs256735	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2927745	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs34410821	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35153242	1.00[ASW][hapmap]
rs35470250	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35864326	0.83[EUR][1000 genomes]
rs4344867	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502546	0.86[JPT][hapmap]
rs6508721	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508725	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7247090	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7254009	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs8109103	ZNF781	trans	cerebellum	SCAN
rs8109103	IL29	cis	parietal	SCAN
rs8109103	DMPK	cis	parietal	SCAN
rs8109103	KIAA0961	cis	multi-tissue	Pritchard
rs8109103	AC012309.5	cis	Heart Left Ventricle	GTEx
rs8109103	AC012309.5	cis	Artery Tibial	GTEx
rs8109103	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs8109103	AC012309.5	cis	Esophagus Muscularis	GTEx
rs8109103	HKR1	cis	multi-tissue	Pritchard
rs8109103	EIF3K	cis	parietal	SCAN
rs8109103	PHLDB3	cis	cerebellum	SCAN
rs8109103	CBLC	cis	parietal	SCAN
rs8109103	ZNF226	cis	cerebellum	SCAN
rs8109103	AKT2	cis	parietal	SCAN
rs8109103	PLEKHG2	cis	cerebellum	SCAN
rs8109103	AC012309.5	cis	Thyroid	GTEx
rs8109103	HIPK4	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37984800-37996400	Weak transcription	Fetal Heart	heart
2	chr19:37989000-37996200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:37989000-37996800	Weak transcription	Left Ventricle	heart
4	chr19:37989000-37996800	Weak transcription	Ovary	ovary
5	chr19:37989200-37996400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:37991200-37996800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr19:37991400-37996000	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:37992000-37996400	Weak transcription	Brain Anterior Caudate	brain
9	chr19:37992000-37996600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:37992200-37996400	Weak transcription	Fetal Brain Female	brain
11	chr19:37992200-37996600	Weak transcription	Aorta	Aorta
12	chr19:37992400-37995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:37992600-37994800	Weak transcription	Fetal Muscle Leg	muscle
14	chr19:37992600-37995000	Weak transcription	Fetal Stomach	stomach
15	chr19:37992800-37996400	Weak transcription	Fetal Kidney	kidney
16	chr19:37993000-37996800	Weak transcription	Right Atrium	heart
17	chr19:37993200-37996200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:37993200-37996200	Weak transcription	Fetal Intestine Large	intestine
19	chr19:37993200-37996800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:37993400-37994800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:37993400-37995600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:37993400-37996400	Weak transcription	Brain Germinal Matrix	brain
23	chr19:37993600-37996200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:37993600-37996200	Weak transcription	Primary T cells from cord blood	blood
25	chr19:37993600-37996400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:37993800-37996200	Weak transcription	Primary B cells from cord blood	blood
27	chr19:37993800-37996400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:37993800-37996600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:37994000-37996200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:37994000-37996200	Weak transcription	Right Ventricle	heart
31	chr19:37994000-37996200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:37994000-37996600	Weak transcription	Rectal Mucosa Donor 31	rectum

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