Variant report

Variant	rs11717842
Chromosome Location	chr3:141208684-141208685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141208093..141210015-chr3:141222017..141224626,2	MCF-7	breast:
2	chr3:141208057..141209932-chr3:141278258..141280316,2	MCF-7	breast:
3	chr3:141189849..141195094-chr3:141204829..141208801,7	MCF-7	breast:
4	chr3:141206890..141209130-chr3:141222372..141224478,3	MCF-7	breast:
5	chr3:141205894..141211656-chr3:141222007..141226023,7	K562	blood:

Variant related genes	Relation type
ENSG00000215606	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1077181	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes]
rs11557453	0.84[CEU][hapmap]
rs11707656	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708253	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709875	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711318	0.92[EUR][1000 genomes]
rs11713714	0.84[EUR][1000 genomes]
rs11714208	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs11716776	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12695734	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695736	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695740	0.92[CEU][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs12695741	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12695743	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs13059128	0.84[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes]
rs13068454	0.85[EUR][1000 genomes]
rs13072100	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]
rs13078872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084444	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]
rs13088429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095168	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13098300	0.88[AMR][1000 genomes]
rs13099945	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1863870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312194	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2312266	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34317570	0.94[EUR][1000 genomes]
rs34342794	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3806647	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4334619	0.83[EUR][1000 genomes]
rs71619392	0.92[EUR][1000 genomes]
rs720663	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7636914	1.00[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs7651511	0.94[EUR][1000 genomes]
rs9289629	0.92[CEU][hapmap];0.85[MEX][hapmap]
rs9289634	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9808953	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9822575	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs9823528	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9829588	0.85[EUR][1000 genomes]
rs9830055	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs9833121	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs9836050	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs9836818	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838230	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9838419	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840159	0.83[EUR][1000 genomes]
rs9840697	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9843866	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9849180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850416	0.96[CEU][hapmap];0.85[MEX][hapmap];0.93[EUR][1000 genomes]
rs9865971	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868956	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870749	0.96[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11717842	ATP1B3	cis	cerebellum	SCAN
rs11717842	ATR	cis	parietal	SCAN
rs11717842	GK5	cis	parietal	SCAN
rs11717842	ZBTB38	cis	cerebellum	SCAN
rs11717842	RASA2	cis	cerebellum	SCAN
rs11717842	RASA2	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141206800-141217400	Weak transcription	Spleen	Spleen
2	chr3:141207000-141209400	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr3:141207000-141216600	Weak transcription	Small Intestine	intestine
4	chr3:141207000-141217400	Weak transcription	Left Ventricle	heart
5	chr3:141207000-141235800	Weak transcription	Gastric	stomach
6	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
7	chr3:141207200-141209200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr3:141207200-141217400	Weak transcription	Psoas Muscle	Psoas
9	chr3:141207400-141209000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:141207400-141209000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:141207400-141209200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:141207400-141209200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:141207400-141209200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:141207400-141209200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:141207400-141209400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:141207400-141209400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:141207400-141209600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:141207400-141209600	Genic enhancers	Fetal Thymus	thymus
19	chr3:141207400-141209800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:141207400-141209800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:141207400-141210000	Weak transcription	NHLF	lung
22	chr3:141207400-141210200	Weak transcription	HSMMtube	muscle
23	chr3:141207400-141210400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr3:141207400-141211600	Weak transcription	Fetal Brain Male	brain
25	chr3:141207400-141213000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:141207400-141215000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:141207400-141217200	Weak transcription	Fetal Heart	heart
28	chr3:141207400-141217400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:141207400-141217600	Weak transcription	Colonic Mucosa	Colon
30	chr3:141207400-141231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:141207600-141208800	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:141207600-141209600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:141207800-141208800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:141207800-141208800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:141207800-141209000	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:141207800-141210400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr3:141207800-141211000	Weak transcription	Fetal Kidney	kidney
38	chr3:141207800-141217400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:141207800-141233200	Weak transcription	Fetal Intestine Large	intestine
40	chr3:141207800-141235600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:141208000-141208800	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:141208000-141209200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:141208000-141209200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:141208000-141209400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr3:141208000-141209400	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:141208000-141209800	Enhancers	Thymus	Thymus
47	chr3:141208000-141210000	Weak transcription	A549	lung
48	chr3:141208000-141210200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:141208000-141210200	Enhancers	K562	blood
50	chr3:141208000-141210400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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