Variant report

Variant	rs2300185
Chromosome Location	chr20:1135413-1135414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2072965	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2300186	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3087751	0.90[LWK][hapmap];0.80[YRI][hapmap]
rs3746814	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4813044	0.96[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4813945	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6040199	0.90[LWK][hapmap];0.80[YRI][hapmap]
rs6040222	0.90[JPT][hapmap]
rs6040293	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6074191	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6077930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134051	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1065838	chr20:866302-1147601	Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv544139	chr20:866302-1147601	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1055328	chr20:867911-1145765	Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1059611	chr20:867911-1158694	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv544140	chr20:867911-1158694	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv949356	chr20:961527-1135413	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv1799982	chr20:1097289-1136252	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2300185	DCP1B	trans	cerebellum	SCAN
rs2300185	LOC644845	trans	multi-tissue	Pritchard
rs2300185	C20orf54	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1100400-1146600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1104600-1135800	Strong transcription	Dnd41	blood
3	chr20:1112200-1137400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:1114000-1138000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:1115200-1153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:1115800-1137800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr20:1116000-1141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr20:1116600-1144600	Weak transcription	Stomach Mucosa	stomach
11	chr20:1116800-1141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr20:1117000-1141200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr20:1117000-1141600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:1117200-1144600	Weak transcription	Hela-S3	cervix
15	chr20:1118000-1135600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr20:1121000-1140800	Weak transcription	K562	blood
17	chr20:1121200-1140400	Weak transcription	NH-A	brain
18	chr20:1121400-1144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr20:1121800-1141200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr20:1124000-1136600	Strong transcription	Primary B cells from cord blood	blood
21	chr20:1124000-1136600	Strong transcription	Primary T cells from cord blood	blood
22	chr20:1125800-1138200	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr20:1127200-1141200	Weak transcription	HUVEC	blood vessel
24	chr20:1127200-1143800	Weak transcription	Colon Smooth Muscle	Colon
25	chr20:1127400-1141400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:1128000-1135600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr20:1128000-1140600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr20:1128200-1135600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr20:1128200-1141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:1128400-1135600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:1128400-1135800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr20:1128400-1140600	Weak transcription	Brain Angular Gyrus	brain
33	chr20:1128600-1135800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr20:1128600-1140800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr20:1128800-1135800	Weak transcription	Spleen	Spleen
36	chr20:1128800-1136000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:1128800-1140400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:1128800-1141200	Weak transcription	Gastric	stomach
39	chr20:1128800-1141200	Weak transcription	NHLF	lung
40	chr20:1128800-1143800	Weak transcription	Small Intestine	intestine
41	chr20:1129000-1140200	Weak transcription	Colonic Mucosa	Colon
42	chr20:1130000-1157800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr20:1130800-1136400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr20:1130800-1139600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr20:1131200-1145800	Strong transcription	HepG2	liver
46	chr20:1131400-1136800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr20:1131600-1137200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr20:1131600-1138000	Strong transcription	Placenta	Placenta
49	chr20:1131800-1136000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr20:1131800-1136800	Strong transcription	Fetal Muscle Trunk	muscle

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