Variant report

Variant	rs7627807
Chromosome Location	chr3:141243728-141243729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141204551..141207938-chr3:141241119..141245308,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.88[JPT][hapmap]
rs1493209	0.88[JPT][hapmap]
rs1493210	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16851483	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]
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];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2035936	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2639997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2640017	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs295299	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs295300	0.84[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs295320	0.88[JPT][hapmap]
rs295321	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34558081	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821709	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]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683612	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58025624	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60654199	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61750362	0.80[AFR][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	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7618787	0.90[ASW][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7627807	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
2	chr3:141210400-141248000	Weak transcription	NHLF	lung
3	chr3:141217800-141258400	Weak transcription	Psoas Muscle	Psoas
4	chr3:141226600-141254400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:141228400-141246600	Strong transcription	Dnd41	blood
6	chr3:141229400-141267400	Weak transcription	Fetal Heart	heart
7	chr3:141230000-141259800	Weak transcription	Small Intestine	intestine
8	chr3:141231200-141245000	Strong transcription	Fetal Thymus	thymus
9	chr3:141231600-141254400	Weak transcription	Fetal Kidney	kidney
10	chr3:141231600-141263600	Weak transcription	Fetal Brain Male	brain
11	chr3:141232200-141245600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:141232200-141254400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:141232600-141244400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:141234000-141254400	Weak transcription	Right Ventricle	heart
15	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:141236400-141244200	Weak transcription	Pancreas	Pancrea
17	chr3:141236400-141245200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:141236400-141249000	Weak transcription	Right Atrium	heart
19	chr3:141236400-141254400	Weak transcription	Brain Angular Gyrus	brain
20	chr3:141236400-141254400	Weak transcription	Left Ventricle	heart
21	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
23	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:141236600-141244200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:141236600-141244200	Weak transcription	Liver	Liver
26	chr3:141236600-141244600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:141236600-141244800	Weak transcription	Colonic Mucosa	Colon
28	chr3:141236600-141247600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:141236600-141247800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:141236600-141248400	Weak transcription	Adipose Nuclei	Adipose
31	chr3:141236600-141254400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:141236600-141254400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:141236600-141254400	Weak transcription	Esophagus	oesophagus
34	chr3:141236600-141263200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:141236600-141275800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:141236600-141299400	Weak transcription	Gastric	stomach
38	chr3:141237000-141248600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:141237000-141265400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:141238000-141245600	Weak transcription	HMEC	breast
42	chr3:141238400-141244800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:141238600-141253800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:141239400-141245400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:141239400-141254400	Weak transcription	Placenta	Placenta
46	chr3:141239800-141244800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:141240000-141245400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:141240000-141245400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:141240000-141247800	Weak transcription	NHDF-Ad	bronchial
50	chr3:141240000-141249200	Weak transcription	Fetal Lung	lung

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