Variant report

Variant	rs3821709
Chromosome Location	chr3:141280273-141280274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141178423..141179603-chr3:141279621..141280965,17	MCF-7	breast:
2	chr3:141279958..141280759-chr3:141363300..141364055,4	K562	blood:
3	chr3:141030314..141031238-chr3:141279893..141280648,9	K562	blood:
4	chr3:141178686..141179587-chr3:141280024..141280748,3	MCF-7	breast:
5	chr3:141192768..141193780-chr3:141279858..141280853,7	MCF-7	breast:
6	chr3:141177945..141179663-chr3:141279624..141280925,17	K562	blood:
7	chr3:141178968..141180548-chr3:141278934..141280564,2	K562	blood:
8	chr3:141279547..141282126-chr3:141289816..141292776,2	K562	blood:
9	chr3:140911179..140911719-chr3:141280024..141280597,2	K562	blood:
10	chr3:141204790..141206476-chr3:141279020..141280958,2	MCF-7	breast:
11	chr3:141022174..141022779-chr3:141279961..141280583,2	MCF-7	breast:
12	chr3:141208057..141209932-chr3:141278258..141280316,2	MCF-7	breast:
13	chr3:141192631..141193903-chr3:141279683..141281016,7	K562	blood:

No data

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	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851438	0.82[JPT][hapmap]
rs16851441	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851483	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]
rs1863867	0.88[JPT][hapmap]
rs2035935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2035936	1.00[ASW][hapmap];0.94[CHB][hapmap];0.97[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];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2639997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.93[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];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs295299	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs295300	0.84[CHB][hapmap];0.83[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];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34558081	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821710	0.87[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683612	0.88[ASN][1000 genomes]
rs58025624	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60654199	0.90[ASN][1000 genomes]
rs6767158	0.87[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.88[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.82[JPT][hapmap]
rs9879503	0.82[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
rs3821709	ZBTB38	cis	multi-tissue	Pritchard
rs3821709	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
3	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:141236600-141299400	Weak transcription	Gastric	stomach
6	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
8	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
9	chr3:141254800-141291400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:141254800-141292200	Weak transcription	Left Ventricle	heart
11	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
15	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:141255200-141304800	Weak transcription	Ovary	ovary
17	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
19	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
20	chr3:141263600-141292000	Weak transcription	Colonic Mucosa	Colon
21	chr3:141263800-141288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:141265000-141290200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:141265200-141283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
25	chr3:141267000-141289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:141267000-141290200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:141267400-141295000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
29	chr3:141269200-141294400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:141271600-141281400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:141272400-141291400	Weak transcription	GM12878-XiMat	blood
33	chr3:141272600-141319200	Strong transcription	Dnd41	blood
34	chr3:141272800-141285800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:141273200-141280600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:141274800-141280400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr3:141275600-141281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:141276000-141281400	Weak transcription	Fetal Stomach	stomach
40	chr3:141276000-141281600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:141276000-141290400	Weak transcription	Brain Germinal Matrix	brain
42	chr3:141276000-141299400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:141276200-141280800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:141276200-141283200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:141276200-141284000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:141276200-141289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:141276200-141289800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:141276200-141290200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:141276200-141291000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:141276200-141291200	Weak transcription	Brain Hippocampus Middle	brain

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