Variant report

Variant	rs590336
Chromosome Location	chr11:73708521-73708522
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:73708329-73708692	GM12891	blood:	n/a	n/a
2	PAX5	chr11:73708104-73708638	GM12878	blood:	n/a	n/a
3	CTCF	chr11:73708480-73708630	GM12864	blood:	n/a	n/a
4	PAX5	chr11:73708151-73708588	GM12878	blood:	n/a	n/a
5	CTCF	chr11:73708480-73708630	GM12872	blood:	n/a	n/a
6	CTCF	chr11:73708520-73708670	GM12874	blood:	n/a	n/a
7	CTCF	chr11:73708460-73708610	GM12875	blood:	n/a	n/a
8	CTCF	chr11:73708520-73708670	GM12871	blood:	n/a	n/a
9	CTCF	chr11:73708520-73708670	GM12875	blood:	n/a	n/a
10	PAX5	chr11:73708043-73708656	GM12878	blood:	n/a	n/a
11	CTCF	chr11:73708440-73708590	GM12865	blood:	n/a	n/a
12	CTCF	chr11:73708460-73708610	GM12872	blood:	n/a	n/a
13	CTCF	chr11:73708520-73708670	GM12864	blood:	n/a	n/a
14	CTCF	chr11:73708520-73708670	GM12866	blood:	n/a	n/a
15	CTCF	chr11:73708520-73708670	GM12873	blood:	n/a	n/a
16	CTCF	chr11:73708500-73708650	GM06990	blood:	n/a	n/a
17	PAX5	chr11:73708178-73708621	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73691320..73695538-chr11:73704392..73710067,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256723	TF binding region
ENSG00000175567	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1685355	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1685356	0.89[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1726744	0.87[JPT][hapmap]
rs1726745	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1726746	0.91[JPT][hapmap]
rs1726764	0.91[JPT][hapmap]
rs1790398	0.87[JPT][hapmap]
rs1790399	0.87[JPT][hapmap]
rs1790404	0.86[JPT][hapmap]
rs2075577	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944036	0.87[JPT][hapmap]
rs588097	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs591758	0.82[CHB][hapmap]
rs631551	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs635441	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647126	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs653529	0.81[CHB][hapmap]
rs659366	0.82[CHB][hapmap]
rs680307	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682602	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7926165	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826033	0.87[JPT][hapmap]
rs826039	0.87[JPT][hapmap]
rs826056	0.86[JPT][hapmap]
rs826061	0.87[JPT][hapmap]
rs826062	0.87[JPT][hapmap]
rs9735789	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs590336	MRPL48	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73695200-73711000	Weak transcription	Fetal Intestine Small	intestine
2	chr11:73702000-73711800	Enhancers	Primary B cells from peripheral blood	blood
3	chr11:73702600-73711800	Weak transcription	Spleen	Spleen
4	chr11:73702800-73708600	Weak transcription	K562	blood
5	chr11:73702800-73711400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:73703000-73710000	Weak transcription	Fetal Muscle Leg	muscle
7	chr11:73703000-73719400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:73704000-73709000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:73706000-73713800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:73706400-73708800	Enhancers	Fetal Thymus	thymus
11	chr11:73706400-73711800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:73706800-73712000	Weak transcription	Fetal Lung	lung
13	chr11:73706800-73713600	Weak transcription	Liver	Liver
14	chr11:73706800-73713800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:73707000-73708800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr11:73707000-73711200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:73707000-73714400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:73707200-73708800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr11:73707200-73709200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:73707200-73709600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:73707200-73711000	Weak transcription	Fetal Brain Female	brain
22	chr11:73707200-73713600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr11:73707200-73714800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:73707400-73708800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:73707400-73709400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:73707400-73709400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr11:73707400-73711400	Enhancers	Primary T cells from cord blood	blood
28	chr11:73707400-73711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:73707400-73711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:73707400-73711800	Enhancers	Primary B cells from cord blood	blood
31	chr11:73707400-73711800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr11:73707400-73713200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr11:73707400-73719800	Weak transcription	Dnd41	blood
34	chr11:73707600-73709800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr11:73707600-73710000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:73707600-73711600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr11:73707600-73711600	Weak transcription	Thymus	Thymus
38	chr11:73707600-73711800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr11:73708000-73708600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr11:73708000-73717600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:73708200-73709200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:73708200-73710200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:73708200-73710800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:73708200-73711400	Weak transcription	Right Ventricle	heart
45	chr11:73708200-73713600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr11:73708400-73708800	Flanking Active TSS	GM12878-XiMat	blood

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