Variant report

Variant	rs13072100
Chromosome Location	chr3:141196647-141196648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141184151..141186428-chr3:141194623..141197205,2	MCF-7	breast:
2	chr3:141172749..141175132-chr3:141195060..141197634,2	K562	blood:
3	chr3:141194536..141196661-chr3:141202566..141205649,3	K562	blood:
4	chr3:141194843..141196913-chr3:141204230..141207024,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1077181	0.92[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11557453	0.84[CEU][hapmap]
rs11707656	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11708253	1.00[AMR][1000 genomes];0.98[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];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711318	0.83[EUR][1000 genomes]
rs11714208	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs11716776	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.96[CEU][hapmap]
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];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695734	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695736	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695740	0.92[CEU][hapmap];0.84[MEX][hapmap]
rs12695741	0.95[CEU][hapmap]
rs12695743	0.88[CEU][hapmap]
rs13059128	0.84[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13068454	0.80[EUR][1000 genomes]
rs13078872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.90[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];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084444	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]
rs13088429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095168	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs13098300	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13099945	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1863870	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312194	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2312266	1.00[ASN][1000 genomes]
rs34317570	0.84[EUR][1000 genomes]
rs34342794	0.85[EUR][1000 genomes]
rs3806647	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71619392	0.82[EUR][1000 genomes]
rs720663	0.96[CEU][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs7636914	0.96[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs7651511	0.84[EUR][1000 genomes]
rs9289629	0.92[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9289634	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9808953	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9822575	0.96[CEU][hapmap];0.85[MEX][hapmap]
rs9823528	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9829588	0.80[EUR][1000 genomes]
rs9830055	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9833121	0.96[CEU][hapmap];0.85[MEX][hapmap]
rs9836050	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9836818	0.85[EUR][1000 genomes]
rs9837202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838230	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9838419	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9840697	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9843866	0.85[EUR][1000 genomes]
rs9849180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850416	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs9865971	0.96[CEU][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs9868956	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9870749	0.96[CEU][hapmap];0.85[MEX][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13072100	ATP1B3	cis	cerebellum	SCAN
rs13072100	ZBTB38	cis	cerebellum	SCAN
rs13072100	RASA2	cis	cerebellum	SCAN
rs13072100	ATR	cis	parietal	SCAN
rs13072100	GK5	cis	parietal	SCAN
rs13072100	RASA2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141184600-141201000	Weak transcription	NHLF	lung
2	chr3:141193200-141197600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:141193200-141198400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:141193600-141197600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:141195400-141196800	Enhancers	HMEC	breast
6	chr3:141195400-141204200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:141195600-141203600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:141195800-141196800	Enhancers	NHEK	skin
9	chr3:141195800-141197000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:141195800-141197000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:141196200-141201200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:141196400-141200600	Weak transcription	Hela-S3	cervix
13	chr3:141196400-141200800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:141196600-141197000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:141196600-141197800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:141196600-141198000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:141196600-141200600	Weak transcription	A549	lung
18	chr3:141196600-141200600	Weak transcription	HUVEC	blood vessel
19	chr3:141196600-141200600	Weak transcription	NHDF-Ad	bronchial
20	chr3:141196600-141200800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:141196600-141200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:141196600-141201200	Weak transcription	Osteobl	bone
23	chr3:141196600-141201400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:141196600-141201800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:141196600-141204400	Weak transcription	NH-A	brain

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