Variant report

Variant	rs539343
Chromosome Location	chr11:74154790-74154791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74153484..74156082-chr11:74157168..74159879,2	K562	blood:
2	chr11:73979603..73981610-chr11:74153903..74155501,2	MCF-7	breast:
3	chr11:74099605..74100422-chr11:74153909..74154835,7	MCF-7	breast:
4	chr11:74100543..74103930-chr11:74153911..74157152,3	MCF-7	breast:
5	chr11:74153867..74156607-chr11:74157168..74160666,3	K562	blood:
6	chr11:74108600..74111383-chr11:74152439..74157109,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254631	Chromatin interaction
ENSG00000264402	Chromatin interaction
ENSG00000149380	Chromatin interaction
ENSG00000165434	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10793084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793085	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898989	0.95[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs11236106	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12274367	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281178	0.95[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2276162	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2509535	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132849	0.82[ASN][1000 genomes]
rs3862800	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484447	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515589	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs517303	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520701	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520837	0.84[ASN][1000 genomes]
rs537637	0.86[ASN][1000 genomes]
rs538805	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs540279	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544747	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56373920	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591372	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603502	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612040	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612700	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs615593	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618993	0.81[ASN][1000 genomes]
rs61901485	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621109	0.85[ASN][1000 genomes]
rs621857	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629134	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633568	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs638656	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs642033	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs642500	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs645184	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs658950	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs670722	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs670829	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs671946	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684028	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685684	0.82[ASN][1000 genomes]
rs692809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694638	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7925353	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947671	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555443	chr11:74109166-74180489	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1041154	chr11:74114801-74177909	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv393	chr11:74135862-74181417	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs539343	INTS4	cis	cerebellum	SCAN
rs539343	PGM2L1	cis	parietal	SCAN
rs539343	SLCO2B1	cis	cerebellum	SCAN
rs539343	PGM2L1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74138800-74161600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74152400-74156200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr11:74152600-74155600	Enhancers	Fetal Intestine Large	intestine
4	chr11:74153200-74155800	Enhancers	Fetal Intestine Small	intestine
5	chr11:74153400-74154800	Enhancers	Aorta	Aorta
6	chr11:74153400-74155200	Enhancers	A549	lung
7	chr11:74153400-74155600	Enhancers	Duodenum Mucosa	Duodenum
8	chr11:74153400-74155600	Enhancers	Stomach Mucosa	stomach
9	chr11:74153400-74155600	Enhancers	K562	blood
10	chr11:74153400-74156800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr11:74153600-74154800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:74153600-74154800	Enhancers	Hela-S3	cervix
13	chr11:74153600-74154800	Enhancers	Osteobl	bone
14	chr11:74153600-74155000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:74153600-74158400	Enhancers	Fetal Muscle Leg	muscle
16	chr11:74153800-74155000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:74154000-74154800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr11:74154000-74154800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr11:74154000-74154800	Enhancers	Fetal Thymus	thymus
20	chr11:74154000-74155000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr11:74154000-74155000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:74154000-74155200	Enhancers	Colonic Mucosa	Colon
23	chr11:74154000-74155800	Enhancers	HSMM	muscle
24	chr11:74154200-74154800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:74154200-74154800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr11:74154200-74154800	Enhancers	Fetal Kidney	kidney
27	chr11:74154200-74154800	Enhancers	Small Intestine	intestine
28	chr11:74154200-74155000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr11:74154200-74155000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr11:74154200-74155200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:74154200-74155800	Enhancers	HSMMtube	muscle
32	chr11:74154200-74156600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr11:74154400-74154800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr11:74154400-74155400	Weak transcription	Pancreas	Pancrea
35	chr11:74154400-74155600	Weak transcription	Psoas Muscle	Psoas
36	chr11:74154400-74160200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:74154400-74167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:74154600-74154800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr11:74154600-74155000	Active TSS	Ovary	ovary
40	chr11:74154600-74155400	Weak transcription	Colon Smooth Muscle	Colon
41	chr11:74154600-74155600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr11:74154600-74167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:74154600-74167800	Weak transcription	Liver	Liver

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