Variant report

Variant	rs11945562
Chromosome Location	chr4:48486598-48486599
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	chr4:48484114..48487251-chr4:48504187..48509460,5	K562	blood:
2	chr4:48485954..48488857-chr4:48528912..48531083,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10018344	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10029732	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10029785	0.86[JPT][hapmap]
rs10030853	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10031777	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10938534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10938537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes]
rs11728565	0.86[AMR][1000 genomes]
rs11734019	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11737677	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes]
rs11933919	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12503599	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12645501	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12645951	0.86[JPT][hapmap]
rs13108474	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13119041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs13127730	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13138269	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13151534	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1472967	0.86[JPT][hapmap]
rs1507862	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1507865	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs16861305	0.82[EUR][1000 genomes]
rs17575720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17656040	0.80[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs17656076	0.80[EUR][1000 genomes]
rs17656094	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1876469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2089503	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2102397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2291474	0.86[JPT][hapmap]
rs2291475	0.86[JPT][hapmap]
rs2292231	0.91[AMR][1000 genomes]
rs2354348	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28470767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34558821	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34635008	0.80[EUR][1000 genomes]
rs392187	0.86[JPT][hapmap]
rs404445	0.86[JPT][hapmap]
rs411261	0.86[JPT][hapmap]
rs421833	0.86[JPT][hapmap]
rs4536901	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs4695391	0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs59686413	0.80[EUR][1000 genomes]
rs62311296	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447640	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447645	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6447647	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6811148	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6816010	0.86[JPT][hapmap]
rs6819159	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6821277	0.86[JPT][hapmap]
rs6829144	0.89[ASN][1000 genomes]
rs6829716	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6836632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6843340	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6848073	0.91[JPT][hapmap]
rs6855022	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6856448	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7438704	0.85[JPT][hapmap]
rs7654770	0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661515	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7667288	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs7678379	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7679210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7683398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7693461	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7697851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs776584	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs776590	0.80[EUR][1000 genomes]
rs776591	0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs796555	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs937888	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs937889	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs952289	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9884546	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs992423	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3421012	chr4:48483395-48487593	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11945562	SLC10A4	cis	lung	GTEx
rs11945562	OCIAD2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48484600-48486600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:48484600-48486600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:48484800-48486600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr4:48484800-48487200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr4:48484800-48487200	Active TSS	A549	lung
6	chr4:48485000-48486600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:48485000-48486600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:48485000-48486600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:48485000-48486600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
10	chr4:48485000-48486600	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr4:48485000-48486800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr4:48485000-48486800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:48485000-48486800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
14	chr4:48485000-48488800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:48485200-48486800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
16	chr4:48485200-48490200	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr4:48485600-48486800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr4:48485800-48486600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:48485800-48486600	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:48485800-48486600	Bivalent Enhancer	Fetal Thymus	thymus
21	chr4:48485800-48486800	Bivalent Enhancer	Spleen	Spleen
22	chr4:48485800-48487200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
23	chr4:48486000-48486600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr4:48486000-48486600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr4:48486000-48486800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:48486000-48487000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:48486000-48487000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:48486200-48486600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:48486200-48486600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:48486200-48486600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
31	chr4:48486200-48486600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
32	chr4:48486200-48486600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
33	chr4:48486200-48486600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:48486200-48486600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:48486200-48486600	Enhancers	Pancreas	Pancrea
36	chr4:48486200-48486800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
37	chr4:48486200-48486800	Bivalent Enhancer	Esophagus	oesophagus
38	chr4:48486200-48486800	Enhancers	Lung	lung
39	chr4:48486200-48487000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
40	chr4:48486200-48487000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:48486200-48487400	Flanking Active TSS	K562	blood
42	chr4:48486200-48492000	Weak transcription	Aorta	Aorta
43	chr4:48486400-48486600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr4:48486400-48486600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
45	chr4:48486400-48486600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr4:48486400-48486600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr4:48486400-48486600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:48486400-48486600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr4:48486400-48486600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr4:48486400-48486600	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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