Variant report

Variant	rs11133443
Chromosome Location	chr4:57336309-57336310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr4:57336301-57336314	GM12878	blood:	n/a	n/a
2	FOS	chr4:57336153-57336348	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF384	chr4:57335838-57336363	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57334621..57337468-chr4:57366931..57368856,2	K562	blood:
2	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
3	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
4	chr4:57300392..57305074-chr4:57333261..57337861,17	MCF-7	breast:
5	chr4:57335761..57337736-chr4:57343152..57345663,2	MCF-7	breast:
6	chr4:57334260..57336507-chr4:57410772..57412509,2	K562	blood:
7	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
8	chr4:57333899..57336357-chr4:57340358..57342235,2	MCF-7	breast:

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10010544	0.86[ASN][1000 genomes]
rs10434444	1.00[CEU][hapmap]
rs1060472	0.89[TSI][hapmap]
rs11133442	0.89[TSI][hapmap]
rs12498340	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs12501502	0.80[TSI][hapmap]
rs12645138	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1520026	0.80[TSI][hapmap]
rs17086696	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs1967559	0.83[TSI][hapmap]
rs1983378	1.00[CEU][hapmap]
rs2271923	0.80[TSI][hapmap]
rs2271925	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34510373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796548	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3822001	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4493603	0.80[TSI][hapmap]
rs4565139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864579	1.00[CEU][hapmap]
rs4865092	1.00[CEU][hapmap]
rs56066795	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56356367	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56672277	0.90[ASN][1000 genomes]
rs59997251	0.82[ASN][1000 genomes]
rs60104031	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554344	0.92[CEU][hapmap]
rs67343558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67721941	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6853418	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73167398	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7664841	0.89[TSI][hapmap]
rs7696808	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8340	1.00[CEU][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11133443	SRP72	cis	normal skin	skin_eQTL
rs11133443	AASDH	cis	cerebellum	SCAN
rs11133443	AASDH	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57334200-57336400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:57334800-57336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57334800-57336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:57334800-57336400	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:57334800-57336400	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr4:57334800-57336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:57334800-57336400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:57334800-57336600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr4:57334800-57336600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:57334800-57337800	Weak transcription	Esophagus	oesophagus
11	chr4:57334800-57337800	Weak transcription	Gastric	stomach
12	chr4:57334800-57337800	Weak transcription	Pancreas	Pancrea
13	chr4:57334800-57338000	Weak transcription	Lung	lung
14	chr4:57334800-57340200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:57334800-57340200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:57334800-57340200	Weak transcription	Left Ventricle	heart
17	chr4:57334800-57340200	Weak transcription	Small Intestine	intestine
18	chr4:57334800-57340200	Weak transcription	Spleen	Spleen
19	chr4:57334800-57353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr4:57334800-57364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:57334800-57371200	Weak transcription	Stomach Mucosa	stomach
22	chr4:57335000-57336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:57335000-57336400	Weak transcription	Fetal Stomach	stomach
24	chr4:57335000-57337600	Weak transcription	Ovary	ovary
25	chr4:57335000-57337800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr4:57335000-57337800	Weak transcription	Thymus	Thymus
27	chr4:57335000-57340200	Weak transcription	Aorta	Aorta
28	chr4:57335000-57340800	Weak transcription	Colonic Mucosa	Colon
29	chr4:57335000-57354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:57335200-57336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:57335200-57336400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:57335200-57336400	Weak transcription	Fetal Intestine Small	intestine
33	chr4:57335200-57336400	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:57335200-57336400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:57335200-57336600	Enhancers	Primary T cells from cord blood	blood
36	chr4:57335200-57336600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:57335200-57336600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:57335200-57336600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:57335200-57336600	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:57335200-57337800	Weak transcription	Brain Angular Gyrus	brain
41	chr4:57335200-57337800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:57335200-57337800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:57335200-57337800	Weak transcription	HSMMtube	muscle
44	chr4:57335200-57338000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:57335200-57340200	Weak transcription	Psoas Muscle	Psoas
46	chr4:57335200-57340200	Weak transcription	Right Ventricle	heart
47	chr4:57335200-57371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:57335400-57336400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr4:57335400-57337200	Weak transcription	HSMM	muscle
50	chr4:57335400-57337600	Weak transcription	Rectal Mucosa Donor 31	rectum

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