Variant report

Variant	rs6040222
Chromosome Location	chr20:1140727-1140728
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1140369-1142381	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1138646..1140919-chr20:1161486..1163038,2	K562	blood:

Variant related genes	Relation type
ACTG1P3	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1053653	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2072965	0.81[JPT][hapmap]
rs2300185	0.90[JPT][hapmap]
rs2300186	0.85[JPT][hapmap]
rs3746814	0.81[ASN][1000 genomes]
rs4813044	0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4813945	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs5001787	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs6040197	0.81[YRI][hapmap]
rs6074191	0.90[JPT][hapmap]
rs6134051	0.83[JPT][hapmap]
rs62186930	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7273195	0.95[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6040222	LOC644845	trans	multi-tissue	Pritchard

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	chr20:1112400-1154800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr20:1113800-1159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:1115200-1153600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:1116000-1141400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:1116600-1144600	Weak transcription	Stomach Mucosa	stomach
7	chr20:1116800-1141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:1117000-1141200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr20:1117000-1141600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:1117200-1144600	Weak transcription	Hela-S3	cervix
11	chr20:1121000-1140800	Weak transcription	K562	blood
12	chr20:1121400-1144600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:1121800-1141200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr20:1127200-1141200	Weak transcription	HUVEC	blood vessel
15	chr20:1127200-1143800	Weak transcription	Colon Smooth Muscle	Colon
16	chr20:1127400-1141400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr20:1128200-1141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr20:1128600-1140800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr20:1128800-1141200	Weak transcription	Gastric	stomach
20	chr20:1128800-1141200	Weak transcription	NHLF	lung
21	chr20:1128800-1143800	Weak transcription	Small Intestine	intestine
22	chr20:1130000-1157800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr20:1131200-1145800	Strong transcription	HepG2	liver
24	chr20:1132000-1152000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr20:1132200-1142600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr20:1133800-1153800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:1134200-1140800	Weak transcription	Fetal Brain Female	brain
28	chr20:1134200-1141200	Weak transcription	Psoas Muscle	Psoas
29	chr20:1134200-1145600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr20:1134400-1141000	Weak transcription	NHEK	skin
31	chr20:1135400-1141000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr20:1135600-1144200	Weak transcription	Fetal Kidney	kidney
33	chr20:1135600-1159800	Weak transcription	Fetal Heart	heart
34	chr20:1136000-1141400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr20:1136200-1141200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:1136200-1143600	Weak transcription	NHDF-Ad	bronchial
37	chr20:1136200-1144000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr20:1136400-1141200	Weak transcription	Aorta	Aorta
39	chr20:1136400-1141200	Weak transcription	Left Ventricle	heart
40	chr20:1136400-1141800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr20:1136400-1141800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr20:1136400-1143600	Weak transcription	Fetal Brain Male	brain
43	chr20:1136600-1146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr20:1137200-1141200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr20:1137200-1148600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr20:1137200-1154400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr20:1137400-1142600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr20:1137400-1157800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr20:1137400-1157800	Strong transcription	Thymus	Thymus
50	chr20:1137400-1159200	Strong transcription	Primary T cells from cord blood	blood

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