Variant report

Variant	rs1040974
Chromosome Location	chr20:1268250-1268251
allele	A/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	chr20:1268133..1270306-chr20:1306878..1308946,2	MCF-7	breast:
3	chr20:1262142..1267228-chr20:1267583..1271633,5	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1010870	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12481700	0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1323132	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323133	0.99[ASN][1000 genomes]
rs1323134	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1407767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555562	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555563	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814066	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs4814078	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs59163041	0.99[ASN][1000 genomes]
rs6033309	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6033312	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033330	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs6041107	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6041121	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6041150	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7261624	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1040974	DEFB132	cis	parietal	SCAN
rs1040974	GNRH2	cis	parietal	SCAN
rs1040974	FKBP1A	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1248000-1271800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
3	chr20:1248200-1277400	Weak transcription	Fetal Stomach	stomach
4	chr20:1248200-1281200	Weak transcription	NHEK	skin
5	chr20:1249000-1281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:1253000-1274800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:1253800-1285400	Weak transcription	Aorta	Aorta
8	chr20:1255400-1271600	Weak transcription	HSMMtube	muscle
9	chr20:1256000-1277800	Weak transcription	Fetal Brain Female	brain
10	chr20:1256400-1277400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:1256800-1281400	Weak transcription	Esophagus	oesophagus
12	chr20:1258600-1269000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:1260000-1272200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr20:1260400-1269200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr20:1261200-1272000	Weak transcription	Osteobl	bone
16	chr20:1261400-1278800	Weak transcription	NHLF	lung
17	chr20:1262400-1272800	Weak transcription	Right Atrium	heart
18	chr20:1262600-1271800	Weak transcription	Left Ventricle	heart
19	chr20:1262800-1268400	Weak transcription	Psoas Muscle	Psoas
20	chr20:1262800-1271800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr20:1263200-1276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:1264200-1273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:1264800-1269200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr20:1264800-1269800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:1264800-1271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:1264800-1274800	Weak transcription	Gastric	stomach
27	chr20:1265400-1271600	Weak transcription	Lung	lung
28	chr20:1265400-1277800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr20:1265600-1280400	Weak transcription	K562	blood
30	chr20:1266200-1268600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr20:1266200-1268800	Enhancers	Fetal Thymus	thymus
32	chr20:1266400-1284800	Weak transcription	Brain Germinal Matrix	brain
33	chr20:1266800-1268600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:1266800-1269200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr20:1267000-1269200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr20:1267000-1269400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr20:1267200-1269000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:1267200-1281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr20:1267400-1268400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr20:1267400-1268400	Weak transcription	Right Ventricle	heart
41	chr20:1267400-1268400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr20:1267400-1268600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:1267400-1268600	Enhancers	GM12878-XiMat	blood
44	chr20:1267400-1271600	Weak transcription	Fetal Muscle Leg	muscle
45	chr20:1267400-1281000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr20:1267600-1268600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr20:1267600-1271600	Weak transcription	Brain Angular Gyrus	brain
48	chr20:1267600-1281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr20:1267800-1268600	Weak transcription	Brain Anterior Caudate	brain
50	chr20:1267800-1271600	Weak transcription	Brain Inferior Temporal Lobe	brain

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