Variant report

Variant	rs11945978
Chromosome Location	chr4:48178814-48178815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48177121..48180289-chr4:48181668..48184747,3	MCF-7	breast:
2	chr4:48169322..48172122-chr4:48178324..48180864,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1008277	0.92[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10805164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10805165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10938522	0.91[EUR][1000 genomes]
rs11730441	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11733531	0.89[EUR][1000 genomes]
rs11941829	0.89[EUR][1000 genomes]
rs12499541	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[ASN][1000 genomes]
rs12502268	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502528	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs12512766	0.84[ASN][1000 genomes]
rs12512837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649067	0.95[EUR][1000 genomes]
rs13104849	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs13146998	0.92[EUR][1000 genomes]
rs1466990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1466991	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466992	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466994	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507919	1.00[JPT][hapmap]
rs1961974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071027	0.88[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs2089509	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089510	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2089511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243840	1.00[JPT][hapmap]
rs2256425	0.99[EUR][1000 genomes]
rs2271173	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271174	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2661529	1.00[JPT][hapmap]
rs2661543	0.84[ASN][1000 genomes]
rs2661544	0.84[ASN][1000 genomes]
rs2661547	1.00[JPT][hapmap]
rs2661548	1.00[JPT][hapmap]
rs2704399	1.00[JPT][hapmap]
rs2704426	1.00[JPT][hapmap]
rs2704433	0.84[ASN][1000 genomes]
rs2704436	0.85[JPT][hapmap]
rs34990592	0.88[EUR][1000 genomes]
rs3792620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792621	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792622	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805179	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805184	1.00[JPT][hapmap]
rs3913948	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4323077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392481	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4392482	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4695339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695340	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695341	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4695342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695344	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695348	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695349	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695350	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61326763	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62309327	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447616	1.00[JPT][hapmap]
rs6814443	1.00[JPT][hapmap]
rs6844543	0.92[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs6845941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6851861	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858716	0.89[EUR][1000 genomes]
rs7654108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668350	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671720	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7680519	0.90[EUR][1000 genomes]
rs7689953	1.00[JPT][hapmap]
rs7695902	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885443	0.92[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs955691	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1006853	chr4:48164958-48196335	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1011820	chr4:48170669-48186729	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1011366	chr4:48173947-48186644	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1005668	chr4:48173947-48186729	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11945978	NFXL1	cis	multi-tissue	Pritchard
rs11945978	FRYL	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48157800-48181000	Weak transcription	Pancreas	Pancrea
2	chr4:48158400-48180600	Weak transcription	Spleen	Spleen
3	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
5	chr4:48158600-48179200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:48158600-48179400	Weak transcription	Fetal Intestine Small	intestine
7	chr4:48158800-48180200	Weak transcription	Fetal Thymus	thymus
8	chr4:48166400-48179600	Weak transcription	Thymus	Thymus
9	chr4:48169000-48180600	Weak transcription	Esophagus	oesophagus
10	chr4:48169000-48190000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:48170600-48181200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:48171200-48181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:48173800-48188400	Weak transcription	Lung	lung
14	chr4:48175600-48180600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:48175800-48191600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:48176000-48180600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:48176000-48185200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:48176000-48185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:48176000-48185400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:48176200-48185200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:48176600-48179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:48177400-48179400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:48177600-48179200	Weak transcription	Liver	Liver
24	chr4:48177600-48182200	Weak transcription	HSMM	muscle
25	chr4:48177800-48181600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr4:48178000-48179400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:48178000-48180000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:48178000-48180800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:48178000-48192400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:48178200-48179600	Enhancers	GM12878-XiMat	blood
31	chr4:48178200-48180000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:48178200-48180000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:48178200-48182200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr4:48178200-48185200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:48178800-48179000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:48178800-48180600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:48178800-48185400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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