Variant report

Variant	rs6041107
Chromosome Location	chr20:1264026-1264027
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1264004..1265763-chr20:1267521..1269306,2	K562	blood:
2	chr20:1249007..1251870-chr20:1263248..1267387,3	K562	blood:
3	chr20:1249007..1250962-chr20:1262132..1264748,2	K562	blood:
4	chr20:1262142..1267228-chr20:1267583..1271633,5	K562	blood:
5	chr20:1261527..1264873-chr20:1277243..1279340,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1010870	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1040974	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12481700	0.90[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1323132	0.91[ASN][1000 genomes]
rs1323133	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1323134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1407767	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1555562	0.92[ASN][1000 genomes]
rs1555563	0.91[ASN][1000 genomes]
rs4814066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4814078	0.85[YRI][hapmap]
rs59163041	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6033309	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6033312	0.98[ASN][1000 genomes]
rs6033330	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6041121	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6041150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7261624	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1067360	chr20:1245753-1283508	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1067393	chr20:1254805-1302796	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1248000-1266800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr20:1248000-1271800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
4	chr20:1248200-1265000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr20:1248200-1277400	Weak transcription	Fetal Stomach	stomach
6	chr20:1248200-1281200	Weak transcription	NHEK	skin
7	chr20:1248600-1266800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:1249000-1281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:1251800-1267000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr20:1252000-1264800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:1252000-1267200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr20:1253000-1274800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr20:1253800-1285400	Weak transcription	Aorta	Aorta
14	chr20:1254200-1266800	Weak transcription	Brain Hippocampus Middle	brain
15	chr20:1255400-1271600	Weak transcription	HSMMtube	muscle
16	chr20:1256000-1277800	Weak transcription	Fetal Brain Female	brain
17	chr20:1256400-1277400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr20:1256800-1267000	Weak transcription	Fetal Muscle Leg	muscle
19	chr20:1256800-1281400	Weak transcription	Esophagus	oesophagus
20	chr20:1257600-1266800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr20:1258600-1267000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr20:1258600-1269000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:1260000-1272200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr20:1260400-1265400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr20:1260400-1269200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr20:1260600-1267600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr20:1260800-1264800	Enhancers	Brain Anterior Caudate	brain
28	chr20:1260800-1267000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr20:1261200-1265200	Weak transcription	K562	blood
30	chr20:1261200-1267400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr20:1261200-1272000	Weak transcription	Osteobl	bone
32	chr20:1261400-1278800	Weak transcription	NHLF	lung
33	chr20:1262400-1264600	Weak transcription	Adipose Nuclei	Adipose
34	chr20:1262400-1265800	Weak transcription	Brain Germinal Matrix	brain
35	chr20:1262400-1272800	Weak transcription	Right Atrium	heart
36	chr20:1262600-1265200	Weak transcription	Brain Angular Gyrus	brain
37	chr20:1262600-1266800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:1262600-1271800	Weak transcription	Left Ventricle	heart
39	chr20:1262800-1264600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr20:1262800-1264800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr20:1262800-1267000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr20:1262800-1268400	Weak transcription	Psoas Muscle	Psoas
43	chr20:1262800-1271800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr20:1263200-1264400	Weak transcription	Stomach Mucosa	stomach
45	chr20:1263200-1276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr20:1263400-1265400	Enhancers	Fetal Lung	lung
47	chr20:1263400-1267000	Enhancers	Primary T cells from cord blood	blood
48	chr20:1263600-1264400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr20:1263600-1264800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr20:1263600-1264800	Enhancers	Lung	lung

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