Variant report

Variant	rs2857
Chromosome Location	chr19:36825458-36825459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403738	0.91[CHB][hapmap]
rs10407850	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs10416509	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs10416742	0.91[CHB][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap]
rs10416925	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]
rs12459704	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs12461077	0.81[CHB][hapmap]
rs12461529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462725	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17206379	1.00[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271842	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385802	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945956	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945989	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967508	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967511	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967519	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3098393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111555	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111556	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810326	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4806284	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs56378871	0.88[ASN][1000 genomes]
rs61706074	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112568	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112569	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112631	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112632	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62113869	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251745	0.82[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap]
rs7253122	0.87[ASN][1000 genomes]
rs73043845	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73043902	0.88[ASN][1000 genomes]
rs8104241	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111860	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2857	ZFP82	cis	lymphoblastoid	seeQTL
rs2857	LINC00665	cis	Muscle Skeletal	GTEx
rs2857	ZFP14	cis	lymphoblastoid	seeQTL
rs2857	ZNF781	cis	cerebellum	SCAN
rs2857	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs2857	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs2857	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs2857	KIAA1559	cis	multi-tissue	Pritchard
rs2857	LINC00665	cis	Nerve Tibial	GTEx
rs2857	ZNF527	cis	cerebellum	SCAN
rs2857	ZNF545	cis	multi-tissue	Pritchard
rs2857	ZNF222	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36823000-36826600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr19:36823000-36827400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:36823200-36827400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr19:36823200-36828000	Weak transcription	Left Ventricle	heart
5	chr19:36823200-36830200	Weak transcription	Fetal Brain Male	brain
6	chr19:36823400-36826600	Weak transcription	Fetal Stomach	stomach
7	chr19:36823400-36827200	Weak transcription	Brain Hippocampus Middle	brain
8	chr19:36823400-36827200	Weak transcription	Pancreas	Pancrea
9	chr19:36823400-36827400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:36823400-36827400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:36823400-36827600	Weak transcription	Primary B cells from cord blood	blood
12	chr19:36823400-36827600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:36823400-36828200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:36823400-36828400	Weak transcription	Right Ventricle	heart
15	chr19:36823400-36828600	Weak transcription	Fetal Heart	heart
16	chr19:36823400-36829000	Weak transcription	Placenta	Placenta
17	chr19:36823400-36829200	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:36823400-36830200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:36823400-36830200	Weak transcription	Brain Angular Gyrus	brain
20	chr19:36823400-36830200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:36823400-36830200	Weak transcription	Brain Substantia Nigra	brain
22	chr19:36823400-36830200	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:36823400-36830400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:36823600-36826600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:36823600-36827200	Weak transcription	Adipose Nuclei	Adipose
26	chr19:36823600-36827200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:36823600-36827400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:36823600-36827400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:36823600-36827400	Weak transcription	Fetal Lung	lung
30	chr19:36823600-36827400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:36823600-36827400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:36823600-36827600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:36823600-36827600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:36823600-36827800	Weak transcription	Fetal Kidney	kidney
35	chr19:36823600-36828000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:36823600-36828200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:36823600-36828400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:36823600-36830000	Weak transcription	Brain Anterior Caudate	brain
39	chr19:36823600-36830000	Weak transcription	Brain Germinal Matrix	brain
40	chr19:36823600-36830200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:36823600-36830200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:36823600-36830200	Weak transcription	Fetal Brain Female	brain
43	chr19:36823600-36830200	Weak transcription	Ovary	ovary
44	chr19:36823600-36831400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:36823800-36853600	ZNF genes & repeats	Liver	Liver
46	chr19:36824600-36827200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr19:36824600-36838000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:36825000-36830200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:36825000-36836600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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