Variant report

Variant	rs6785874
Chromosome Location	chr3:141244816-141244817
allele	A/G
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:
2	chr3:141244511..141246249-chr3:141247740..141249337,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB38-1	chr3:141244576-141244963	ENSG00000250170.1

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11711375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11916906	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917587	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062809	0.82[EUR][1000 genomes]
rs13069717	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1366042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1493209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16851435	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2172471	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[EUR][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs295320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs295323	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35711802	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440015	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6763498	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776003	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7612543	0.82[TSI][hapmap]
rs7627807	0.88[JPT][hapmap]
rs7632308	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7643837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289631	0.83[EUR][1000 genomes]
rs9813177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850416	0.82[TSI][hapmap]
rs9851256	0.87[CEU][hapmap]
rs9878347	0.94[JPT][hapmap];0.91[YRI][hapmap]
rs9879503	0.94[JPT][hapmap];0.91[YRI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6785874	ZBTB38	cis	cerebellum	SCAN
rs6785874	RASA2	Cis_1M	lymphoblastoid	RTeQTL
rs6785874	RASA2	cis	parietal	SCAN
rs6785874	RASA2	cis	cerebellum	SCAN
rs6785874	ATP1B3	cis	cerebellum	SCAN
rs6785874	GK5	cis	parietal	SCAN

Chromatin state (count:120 , 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	chr3:141234000-141254400	Weak transcription	Right Ventricle	heart
14	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:141236400-141245200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:141236400-141249000	Weak transcription	Right Atrium	heart
17	chr3:141236400-141254400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:141236400-141254400	Weak transcription	Left Ventricle	heart
19	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:141236600-141247600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:141236600-141247800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:141236600-141248400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:141236600-141254400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:141236600-141254400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:141236600-141254400	Weak transcription	Esophagus	oesophagus
28	chr3:141236600-141263200	Weak transcription	Brain Germinal Matrix	brain
29	chr3:141236600-141275800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:141236600-141299400	Weak transcription	Gastric	stomach
32	chr3:141237000-141248600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:141237000-141265400	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:141238000-141245600	Weak transcription	HMEC	breast
36	chr3:141238600-141253800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:141239400-141245400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:141239400-141254400	Weak transcription	Placenta	Placenta
39	chr3:141240000-141245400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:141240000-141245400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:141240000-141247800	Weak transcription	NHDF-Ad	bronchial
42	chr3:141240000-141249200	Weak transcription	Fetal Lung	lung
43	chr3:141240200-141254400	Weak transcription	K562	blood
44	chr3:141241000-141245200	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr3:141241400-141245000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:141241400-141246000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:141241400-141249400	Weak transcription	HepG2	liver
48	chr3:141241400-141253800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:141241800-141247400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:141241800-141263600	Weak transcription	Fetal Brain Female	brain

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