Variant report

Variant	rs12481700
Chromosome Location	chr20:1275999-1276000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1272718..1276817-chr20:1277279..1280817,5	MCF-7	breast:
2	chr20:1275541..1277248-chr20:1306085..1307627,2	K562	blood:
3	chr20:1274563..1276619-chr20:1279112..1281898,2	K562	blood:
4	chr20:1272392..1273936-chr20:1275888..1278512,2	K562	blood:

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1010870	0.90[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1040974	0.95[CHD][hapmap];0.90[JPT][hapmap]
rs1323133	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1323134	0.89[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs1407767	0.90[JPT][hapmap]
rs2273955	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3803949	0.85[JPT][hapmap];0.83[LWK][hapmap];0.85[YRI][hapmap]
rs4814066	0.90[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4814078	0.87[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59163041	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6033309	0.81[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs6033330	0.87[ASW][hapmap];0.81[CEU][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes]
rs6041107	0.90[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6041121	0.85[JPT][hapmap]
rs6041150	0.87[ASW][hapmap];0.90[CEU][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7261624	0.93[CHD][hapmap];0.85[JPT][hapmap]
rs72620867	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	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
5	nsv912588	chr20:1269588-1300456	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv912589	chr20:1272686-1298397	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12481700	DEFB132	cis	parietal	SCAN
rs12481700	ADRA1D	cis	parietal	SCAN
rs12481700	FKBP1A	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1248000-1278600	Weak transcription	Spleen	Spleen
2	chr20:1248200-1277400	Weak transcription	Fetal Stomach	stomach
3	chr20:1248200-1281200	Weak transcription	NHEK	skin
4	chr20:1249000-1281400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr20:1253800-1285400	Weak transcription	Aorta	Aorta
6	chr20:1256000-1277800	Weak transcription	Fetal Brain Female	brain
7	chr20:1256400-1277400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:1256800-1281400	Weak transcription	Esophagus	oesophagus
9	chr20:1261400-1278800	Weak transcription	NHLF	lung
10	chr20:1263200-1276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:1265400-1277800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr20:1265600-1280400	Weak transcription	K562	blood
13	chr20:1266400-1284800	Weak transcription	Brain Germinal Matrix	brain
14	chr20:1267200-1281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:1267400-1281000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr20:1267600-1281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr20:1267800-1281000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:1268200-1280600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr20:1268200-1280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr20:1268600-1278000	Weak transcription	Primary T cells from cord blood	blood
21	chr20:1269200-1277600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:1269200-1283600	Weak transcription	Right Ventricle	heart
23	chr20:1269400-1283200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr20:1271800-1280000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr20:1271800-1280200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr20:1271800-1280400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr20:1272200-1280000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr20:1272200-1280200	Weak transcription	Fetal Thymus	thymus
29	chr20:1272200-1285400	Weak transcription	Adipose Nuclei	Adipose
30	chr20:1272200-1285400	Weak transcription	Left Ventricle	heart
31	chr20:1272200-1286000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr20:1272400-1276000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr20:1272400-1277200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr20:1272400-1281200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:1272400-1281200	Weak transcription	Osteobl	bone
36	chr20:1272400-1285800	Weak transcription	Fetal Muscle Leg	muscle
37	chr20:1272600-1279600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:1272600-1294000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr20:1272800-1281200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:1272800-1283400	Weak transcription	HSMMtube	muscle
41	chr20:1273000-1276200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:1273000-1281200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr20:1273000-1294000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr20:1273800-1277400	Weak transcription	Colon Smooth Muscle	Colon
45	chr20:1273800-1280200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr20:1274000-1276000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr20:1274200-1276400	Enhancers	Brain Cingulate Gyrus	brain
48	chr20:1274400-1277200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr20:1274400-1280000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr20:1274600-1282200	Strong transcription	Stomach Smooth Muscle	stomach

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