Variant report

Variant	rs9850416
Chromosome Location	chr3:141272216-141272217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141205388..141207186-chr3:141271123..141273570,2	K562	blood:
2	chr3:141271506..141275087-chr3:141275367..141278539,3	K562	blood:
3	chr3:141204544..141206997-chr3:141271122..141272652,2	MCF-7	breast:
4	chr3:141204151..141206600-chr3:141267953..141272642,5	MCF-7	breast:
5	chr3:141204684..141207186-chr3:141271123..141273570,3	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1077181	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs11557453	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11707656	0.86[EUR][1000 genomes]
rs11708253	0.81[EUR][1000 genomes]
rs11709875	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs11711318	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11711375	0.82[TSI][hapmap]
rs11713714	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714208	0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs11716776	0.92[EUR][1000 genomes]
rs11717144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11717842	0.96[CEU][hapmap];0.85[MEX][hapmap];0.93[EUR][1000 genomes]
rs12695734	0.81[EUR][1000 genomes]
rs12695735	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs12695736	0.92[EUR][1000 genomes]
rs12695740	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12695741	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12695743	0.92[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13059128	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs13067519	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13068454	0.81[EUR][1000 genomes]
rs13072100	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs13078872	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13083593	0.96[CEU][hapmap];0.93[MEX][hapmap];0.92[EUR][1000 genomes]
rs13084444	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13088429	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13095168	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13099945	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16846258	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs1863870	0.92[CEU][hapmap];0.85[MEX][hapmap];0.81[EUR][1000 genomes]
rs2312194	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2312266	0.80[EUR][1000 genomes]
rs295320	0.82[TSI][hapmap]
rs34317570	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34342794	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3732872	1.00[JPT][hapmap]
rs3806647	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3821710	0.82[TSI][hapmap]
rs4334619	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60720666	0.84[ASN][1000 genomes]
rs6767158	0.81[TSI][hapmap]
rs6769161	1.00[JPT][hapmap]
rs6785874	0.82[TSI][hapmap]
rs6800122	0.82[TSI][hapmap]
rs6808837	0.82[TSI][hapmap]
rs71619392	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720663	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73869619	0.82[ASN][1000 genomes]
rs73869620	0.82[ASN][1000 genomes]
rs73869622	0.82[ASN][1000 genomes]
rs73869630	0.84[ASN][1000 genomes]
rs7615579	0.84[ASN][1000 genomes]
rs7616978	0.84[ASN][1000 genomes]
rs7617073	0.84[ASN][1000 genomes]
rs7624941	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7636914	0.85[MEX][hapmap]
rs7643837	0.82[TSI][hapmap]
rs7649666	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7651511	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289629	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[ASN][1000 genomes]
rs9289634	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9808953	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9813177	0.82[TSI][hapmap]
rs9822575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9823528	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9829588	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9830055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9833121	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9836050	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9836818	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9837202	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9838230	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9838419	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9840159	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9840697	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9843866	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9849180	0.96[CEU][hapmap];0.93[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9865971	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9868956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870749	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9873042	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9850416	ZBTB38	cis	cerebellum	SCAN
rs9850416	RASA2	cis	parietal	SCAN
rs9850416	ATP1B3	cis	cerebellum	SCAN
rs9850416	GK5	cis	parietal	SCAN
rs9850416	RASA2	cis	cerebellum	SCAN

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	chr3:141242200-141274800	Weak transcription	Lung	lung
10	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
11	chr3:141246000-141278400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:141249200-141274600	Weak transcription	Liver	Liver
13	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
14	chr3:141254800-141274000	Weak transcription	HepG2	liver
15	chr3:141254800-141274600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:141254800-141275000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:141254800-141291400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:141254800-141292200	Weak transcription	Left Ventricle	heart
19	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
23	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:141255000-141274600	Weak transcription	Placenta	Placenta
25	chr3:141255200-141304800	Weak transcription	Ovary	ovary
26	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:141255400-141277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
29	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
30	chr3:141258600-141275000	Weak transcription	HMEC	breast
31	chr3:141260000-141276600	Weak transcription	Hela-S3	cervix
32	chr3:141260800-141276400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:141261400-141278600	Weak transcription	NHLF	lung
34	chr3:141262600-141278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:141263600-141292000	Weak transcription	Colonic Mucosa	Colon
36	chr3:141263800-141288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:141264000-141273400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:141264000-141274600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:141264000-141274800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:141264000-141275000	Weak transcription	Brain Germinal Matrix	brain
41	chr3:141264000-141275800	Weak transcription	NH-A	brain
42	chr3:141264200-141274600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:141264600-141275800	Weak transcription	Fetal Stomach	stomach
44	chr3:141265000-141290200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:141265200-141275600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:141265200-141283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
48	chr3:141266000-141274800	Weak transcription	Fetal Intestine Small	intestine
49	chr3:141266200-141273400	Weak transcription	Fetal Intestine Large	intestine
50	chr3:141266800-141275400	Weak transcription	A549	lung

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