Variant report

Variant	rs13084444
Chromosome Location	chr3:141277651-141277652
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	chr3:141204781..141208531-chr3:141274095..141278968,6	K562	blood:
3	chr3:141178684..141179373-chr3:141276666..141277719,3	K562	blood:
4	chr3:141272702..141275087-chr3:141275367..141277933,2	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1077181	0.92[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs11557453	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs11707656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11708253	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709875	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11711318	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713714	0.85[EUR][1000 genomes]
rs11714208	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs11716776	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11717842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695734	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695736	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695740	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs12695741	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12695743	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13059128	0.84[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs13067519	0.80[EUR][1000 genomes]
rs13068454	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13072100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095168	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13098300	0.82[AMR][1000 genomes]
rs13099945	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1863870	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312194	0.93[EUR][1000 genomes]
rs2312266	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34317570	0.93[EUR][1000 genomes]
rs34342794	0.93[EUR][1000 genomes]
rs3806647	0.92[EUR][1000 genomes]
rs4334619	0.84[EUR][1000 genomes]
rs71619392	0.91[EUR][1000 genomes]
rs720663	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7636914	0.96[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs7651511	0.93[EUR][1000 genomes]
rs9289629	0.92[CEU][hapmap];0.85[MEX][hapmap]
rs9289634	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9808953	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9822575	0.96[CEU][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs9823528	0.93[EUR][1000 genomes]
rs9829588	0.86[EUR][1000 genomes]
rs9830055	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9833121	0.96[CEU][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs9836050	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836818	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9837202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838230	0.93[EUR][1000 genomes]
rs9838419	0.93[EUR][1000 genomes]
rs9840159	0.84[EUR][1000 genomes]
rs9840697	0.93[EUR][1000 genomes]
rs9843866	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9849180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850416	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9865971	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9868956	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9870749	0.96[CEU][hapmap];0.85[MEX][hapmap];0.84[EUR][1000 genomes]
rs9873042	0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13084444	ZBTB38	cis	cerebellum	SCAN
rs13084444	RASA2	cis	cerebellum	SCAN
rs13084444	ATP1B3	cis	cerebellum	SCAN
rs13084444	ATR	cis	parietal	SCAN
rs13084444	GK5	cis	parietal	SCAN
rs13084444	RASA2	cis	parietal	SCAN

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	chr3:141246000-141278400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
10	chr3:141254800-141291400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:141254800-141292200	Weak transcription	Left Ventricle	heart
12	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
16	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:141255200-141304800	Weak transcription	Ovary	ovary
18	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
20	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
21	chr3:141261400-141278600	Weak transcription	NHLF	lung
22	chr3:141262600-141278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:141263600-141292000	Weak transcription	Colonic Mucosa	Colon
24	chr3:141263800-141288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:141265000-141290200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:141265200-141283000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
28	chr3:141266800-141278600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:141267000-141289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:141267000-141290200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:141267400-141278600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:141267400-141295000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
34	chr3:141269200-141294400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
36	chr3:141271600-141281400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:141272200-141280200	Strong transcription	HSMM	muscle
38	chr3:141272400-141291400	Weak transcription	GM12878-XiMat	blood
39	chr3:141272600-141319200	Strong transcription	Dnd41	blood
40	chr3:141272800-141285800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:141273200-141280600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr3:141273800-141280000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr3:141274400-141279800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr3:141274800-141280400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:141275000-141279000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:141275200-141278000	Strong transcription	NHDF-Ad	bronchial
47	chr3:141275400-141278000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:141275600-141281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:141275800-141278000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:141275800-141280000	Strong transcription	NH-A	brain

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