Variant report

Variant	rs16851483
Chromosome Location	chr3:141275436-141275437
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141271506..141275087-chr3:141275367..141278539,3	K562	blood:
2	chr3:141172263..141174697-chr3:141274621..141277258,2	MCF-7	breast:
3	chr3:141204781..141208531-chr3:141274095..141278968,6	K562	blood:
4	chr3:141173863..141176628-chr3:141274663..141277094,3	MCF-7	breast:
5	chr3:141272702..141275087-chr3:141275367..141277933,2	K562	blood:
6	chr3:141206322..141208347-chr3:141274984..141277409,3	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.88[JPT][hapmap]
rs1493209	0.88[JPT][hapmap]
rs1493210	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1863867	0.88[JPT][hapmap]
rs2035935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2035936	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2639997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2640017	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs295299	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs295300	0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs295320	0.88[JPT][hapmap]
rs295321	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34558081	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821709	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683612	0.87[ASN][1000 genomes]
rs58025624	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60654199	0.91[ASN][1000 genomes]
rs6767158	0.88[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.88[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7627807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1014365	chr3:141235379-141282615	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16851483	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL
rs16851483	ZBTB38	cis	multi-tissue	Pritchard

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:141236600-141275800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:141236600-141299400	Weak transcription	Gastric	stomach
8	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
10	chr3:141246000-141278400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
12	chr3:141254800-141291400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:141254800-141292200	Weak transcription	Left Ventricle	heart
14	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
18	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:141255200-141304800	Weak transcription	Ovary	ovary
20	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:141255400-141277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
23	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
24	chr3:141260000-141276600	Weak transcription	Hela-S3	cervix
25	chr3:141260800-141276400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:141261400-141278600	Weak transcription	NHLF	lung
27	chr3:141262600-141278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:141263600-141292000	Weak transcription	Colonic Mucosa	Colon
29	chr3:141263800-141288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:141264000-141275800	Weak transcription	NH-A	brain
31	chr3:141264600-141275800	Weak transcription	Fetal Stomach	stomach
32	chr3:141265000-141290200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:141265200-141275600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:141265200-141283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
36	chr3:141266800-141278600	Weak transcription	Brain Anterior Caudate	brain
37	chr3:141267000-141275800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:141267000-141289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:141267000-141290200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:141267200-141276800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:141267400-141278600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:141267400-141295000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:141268200-141275800	Weak transcription	NHEK	skin
44	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
45	chr3:141269200-141294400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:141269400-141275800	Weak transcription	Fetal Kidney	kidney
47	chr3:141270000-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:141270400-141275800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:141270600-141276000	Weak transcription	Small Intestine	intestine
50	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain

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