Variant report

Variant	rs3108171
Chromosome Location	chr19:37117302-37117303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10402486	0.98[EUR][1000 genomes]
rs10407386	0.85[EUR][1000 genomes]
rs11084862	0.90[EUR][1000 genomes]
rs12610353	0.87[EUR][1000 genomes]
rs1830031	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2033077	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2217081	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2245366	0.80[ASW][hapmap];0.96[YRI][hapmap]
rs2385642	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2385643	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3096617	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3096618	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs3096619	0.84[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs3096622	0.99[EUR][1000 genomes]
rs3096623	0.99[EUR][1000 genomes]
rs3096627	0.98[EUR][1000 genomes]
rs3096628	0.98[EUR][1000 genomes]
rs3096630	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3096631	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3096632	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs3096633	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3096635	0.86[EUR][1000 genomes]
rs3096636	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3108166	0.96[EUR][1000 genomes]
rs3108167	0.99[EUR][1000 genomes]
rs3108168	0.99[EUR][1000 genomes]
rs3108172	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs3108174	0.99[EUR][1000 genomes]
rs3108179	0.87[EUR][1000 genomes]
rs3108181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3108182	0.90[EUR][1000 genomes]
rs3108184	0.90[EUR][1000 genomes]
rs3108185	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs3108186	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs3108187	0.90[EUR][1000 genomes]
rs3108188	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs3108189	0.89[EUR][1000 genomes]
rs3108190	0.90[EUR][1000 genomes]
rs3108191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3108192	0.85[EUR][1000 genomes]
rs3108193	0.96[EUR][1000 genomes]
rs3108196	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs3108197	0.87[EUR][1000 genomes]
rs3108201	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs3108203	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs3108205	0.90[EUR][1000 genomes]
rs3108208	0.98[EUR][1000 genomes]
rs3108209	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes]
rs3108214	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs3108215	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs3108542	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3108543	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108544	0.97[EUR][1000 genomes]
rs3108545	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3108546	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs3108549	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs3108550	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3108552	0.96[EUR][1000 genomes]
rs3108555	0.90[EUR][1000 genomes]
rs3108559	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs3108560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs3108562	0.90[EUR][1000 genomes]
rs3108563	0.90[EUR][1000 genomes]
rs3108564	0.90[EUR][1000 genomes]
rs3108565	0.85[EUR][1000 genomes]
rs3108566	0.87[EUR][1000 genomes]
rs3108567	0.96[EUR][1000 genomes]
rs3108568	0.87[EUR][1000 genomes]
rs3108570	0.87[EUR][1000 genomes]
rs3108572	0.87[EUR][1000 genomes]
rs3108574	0.87[EUR][1000 genomes]
rs3108575	0.87[EUR][1000 genomes]
rs3108576	0.87[EUR][1000 genomes]
rs3108577	0.87[EUR][1000 genomes]
rs3108579	0.87[EUR][1000 genomes]
rs3108580	0.81[ASW][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs3108594	0.97[EUR][1000 genomes]
rs3108596	1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[EUR][1000 genomes]
rs3108597	1.00[CEU][hapmap];0.94[CHB][hapmap];0.98[EUR][1000 genomes]
rs3108598	0.94[CHB][hapmap]
rs3108600	0.98[EUR][1000 genomes]
rs3108602	0.98[EUR][1000 genomes]
rs3108603	0.98[EUR][1000 genomes]
rs3108604	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108607	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3108608	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs3108609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3108610	0.99[EUR][1000 genomes]
rs3111541	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3111542	0.87[EUR][1000 genomes]
rs3111547	0.99[EUR][1000 genomes]
rs3111549	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3111550	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34002069	0.96[EUR][1000 genomes]
rs34395293	0.98[EUR][1000 genomes]
rs4572520	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4806336	0.98[EUR][1000 genomes]
rs7245414	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7248477	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7252957	0.84[EUR][1000 genomes]
rs7256786	0.80[EUR][1000 genomes]
rs7259195	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7259256	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs8105197	0.85[EUR][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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3108171	ZNF404	cis	parietal	SCAN
rs3108171	LOC390940	cis	parietal	SCAN
rs3108171	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs3108171	AC092295.7	cis	Esophagus Muscularis	GTEx
rs3108171	CAPN12	cis	cerebellum	SCAN
rs3108171	CEACAM19	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:37102000-37118600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:37103000-37118600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr19:37104400-37118400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr19:37104400-37125600	ZNF genes & repeats	Brain Germinal Matrix	brain
9	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
11	chr19:37107000-37118600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
12	chr19:37107000-37120400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr19:37107000-37120400	ZNF genes & repeats	Brain Hippocampus Middle	brain
14	chr19:37107000-37125400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:37107000-37134800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr19:37107200-37119800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:37107400-37117800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr19:37107400-37118400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:37107600-37119600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
21	chr19:37107800-37118400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:37107800-37134600	ZNF genes & repeats	Brain Anterior Caudate	brain
23	chr19:37108400-37118400	ZNF genes & repeats	Fetal Muscle Leg	muscle
24	chr19:37108400-37119800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
25	chr19:37109200-37119800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr19:37109200-37120400	ZNF genes & repeats	Dnd41	blood
27	chr19:37109600-37118400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:37110400-37152600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:37111600-37118600	ZNF genes & repeats	Ovary	ovary
30	chr19:37112400-37120800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
31	chr19:37112400-37122200	ZNF genes & repeats	Psoas Muscle	Psoas
32	chr19:37112600-37119600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:37114600-37117600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:37114800-37117400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:37115000-37119600	ZNF genes & repeats	Fetal Brain Male	brain
36	chr19:37115200-37117800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:37115200-37118600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
38	chr19:37115400-37131800	ZNF genes & repeats	Left Ventricle	heart
39	chr19:37115600-37118000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
40	chr19:37115600-37118800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
41	chr19:37115800-37118200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:37115800-37118200	ZNF genes & repeats	Thymus	Thymus
43	chr19:37116200-37119600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr19:37116200-37120200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:37116400-37118400	ZNF genes & repeats	Aorta	Aorta
46	chr19:37116600-37119800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:37116800-37117600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:37116800-37118000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr19:37116800-37118200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
50	chr19:37116800-37118400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--

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