Variant report

Variant	rs515924
Chromosome Location	chr11:74110353-74110354
allele	A/G
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	TBP	chr11:74109271-74110371	K562	blood:	n/a	n/a
2	NRF1	chr11:74109166-74110363	SK-N-SH	brain:	n/a	chr11:74109775-74109786 chr11:74109804-74109815
3	MTA3	chr11:74109507-74110595	GM12878	blood:	n/a	n/a
4	ARID3A	chr11:74109792-74110550	K562	blood:	n/a	n/a
5	SIN3AK20	chr11:74109256-74110420	MCF-7	breast:	n/a	n/a
6	POLR2A	chr11:74108843-74110423	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:74108761-74110441	SK-N-MC	brain:	n/a	n/a
8	SIX5	chr11:74109355-74110367	A549	lung:	n/a	chr11:74109865-74109874 chr11:74109916-74109925 chr11:74109863-74109872
9	POLR2A	chr11:74108437-74110578	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr11:74109018-74110390	PFSK-1	brain:	n/a	n/a
11	MXI1	chr11:74108593-74110752	IMR90	lung:	n/a	n/a
12	ZNF143	chr11:74109469-74110431	K562	blood:	n/a	chr11:74109856-74109874 chr11:74109916-74109925 chr11:74109865-74109874 chr11:74109863-74109872 chr11:74109914-74109923 chr11:74109914-74109932
13	POLR2A	chr11:74109150-74110362	K562	blood:	n/a	n/a
14	POLR2A	chr11:74109150-74110388	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr11:74109063-74110388	HUVEC	blood vessel:	n/a	n/a
16	EP300	chr11:74109627-74110463	K562	blood:	n/a	chr11:74109654-74109668
17	MAZ	chr11:74109058-74110552	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:74108395-74110386	H1-neurons	neurons:	n/a	n/a
19	HCFC1	chr11:74108250-74110787	Hela-S3	cervix:	n/a	n/a
20	MYC	chr11:74109190-74110817	A549	lung:	n/a	n/a
21	ZNF143	chr11:74109331-74110373	GM12878	blood:	n/a	chr11:74109856-74109874 chr11:74109916-74109925 chr11:74109865-74109874 chr11:74109863-74109872 chr11:74109914-74109923 chr11:74109914-74109932
22	BHLHE40	chr11:74109503-74110380	GM12878	blood:	n/a	n/a
23	BRCA1	chr11:74109586-74110384	Hela-S3	cervix:	n/a	n/a
24	MAX	chr11:74108403-74110372	A549	lung:	n/a	n/a
25	POLR2A	chr11:74109276-74110380	MCF10A-Er-Src	breast:	n/a	n/a
26	SREBP1	chr11:74109307-74110578	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:74108751-74110487	HUVEC	blood vessel:	n/a	n/a
28	MYC	chr11:74109291-74110423	K562	blood:	n/a	n/a
29	POLR2A	chr11:74108544-74110604	PBDE	blood:	n/a	n/a
30	REST	chr11:74108119-74110660	H1-neurons	neurons:	n/a	chr11:74109888-74109906 chr11:74109279-74109292 chr11:74109016-74109026 chr11:74109887-74109907
31	MAX	chr11:74109514-74110358	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74108659..74110537-chr11:74118206..74120213,2	K562	blood:

miRNA name	Chromosome Location	mirBase accession
hsa-miR-548al	chr11:74110346-74110367	MIMAT0019024

Variant related genes	Relation type
PGM2L1	TF binding region
ENSG00000255440	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10898975	0.85[CEU][hapmap]
rs10898976	0.85[CEU][hapmap]
rs10898980	0.85[CEU][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs10898984	0.86[EUR][1000 genomes]
rs11236042	0.85[CEU][hapmap]
rs11236043	0.85[CEU][hapmap]
rs11236052	0.84[CEU][hapmap]
rs11236053	0.85[CEU][hapmap]
rs11236063	0.85[CEU][hapmap];0.90[YRI][hapmap]
rs11236071	0.85[CEU][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs11236072	0.82[EUR][1000 genomes]
rs11236077	0.85[CEU][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs11236082	0.83[EUR][1000 genomes]
rs11236083	0.82[EUR][1000 genomes]
rs11236091	0.86[EUR][1000 genomes]
rs11236092	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs11236093	0.87[EUR][1000 genomes]
rs11236096	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12049823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12225215	0.82[EUR][1000 genomes]
rs12278437	0.85[ASN][1000 genomes]
rs1279293	0.92[YRI][hapmap]
rs17132964	0.85[CEU][hapmap];0.92[YRI][hapmap]
rs2282488	0.85[CEU][hapmap]
rs2509531	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2509532	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132913	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132914	0.90[ASN][1000 genomes]
rs3741132	0.85[CEU][hapmap]
rs485578	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs496428	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516683	0.91[ASN][1000 genomes]
rs520464	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573077	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs577245	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585600	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585613	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597113	0.84[CHB][hapmap]
rs599605	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600085	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61258589	0.86[EUR][1000 genomes]
rs61288268	0.82[EUR][1000 genomes]
rs61902404	0.82[EUR][1000 genomes]
rs624049	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628191	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630893	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs633481	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636501	0.91[ASN][1000 genomes]
rs647870	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654028	0.84[CHB][hapmap]
rs676103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677761	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs679618	0.91[ASN][1000 genomes]
rs687958	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924914	0.86[EUR][1000 genomes]
rs7951617	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1049915	chr11:74052264-74126319	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs515924	PPME1	cis	cerebellum	SCAN
rs515924	P4HA3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74107200-74110400	Active TSS	Fetal Brain Female	brain
2	chr11:74107800-74110400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr11:74107800-74110400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:74107800-74110400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:74107800-74110400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:74107800-74110400	Active TSS	Thymus	Thymus
7	chr11:74107800-74110600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:74107800-74110600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr11:74107800-74110600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr11:74107800-74110800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:74108000-74110400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:74108000-74110400	Active TSS	Brain Anterior Caudate	brain
13	chr11:74108000-74110600	Active TSS	Fetal Brain Male	brain
14	chr11:74108000-74110600	Active TSS	Fetal Kidney	kidney
15	chr11:74108000-74110600	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr11:74108200-74110400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr11:74108200-74110400	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr11:74108200-74110400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:74108200-74110400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr11:74108200-74110400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:74108200-74110400	Active TSS	Brain Angular Gyrus	brain
22	chr11:74108200-74110400	Active TSS	Fetal Stomach	stomach
23	chr11:74108200-74110400	Active TSS	HSMM	muscle
24	chr11:74108200-74110600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:74108200-74110600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:74108200-74110600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr11:74108200-74110600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:74108400-74110400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:74108400-74110400	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr11:74108400-74110400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:74108400-74110400	Active TSS	Aorta	Aorta
32	chr11:74108400-74110400	Active TSS	Brain Substantia Nigra	brain
33	chr11:74108400-74110400	Active TSS	Duodenum Mucosa	Duodenum
34	chr11:74108400-74110400	Active TSS	Fetal Intestine Large	intestine
35	chr11:74108400-74110400	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr11:74108400-74110400	Active TSS	Left Ventricle	heart
37	chr11:74108400-74110400	Active TSS	Ovary	ovary
38	chr11:74108400-74110400	Active TSS	Psoas Muscle	Psoas
39	chr11:74108400-74110400	Active TSS	A549	lung
40	chr11:74108400-74110400	Active TSS	NHDF-Ad	bronchial
41	chr11:74108400-74110400	Active TSS	Osteobl	bone
42	chr11:74108400-74110600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:74108400-74110600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:74108600-74110400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:74108600-74110400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:74108600-74110400	Active TSS	Fetal Intestine Small	intestine
47	chr11:74108600-74110400	Active TSS	Pancreas	Pancrea
48	chr11:74108600-74110400	Active TSS	Placenta Amnion	Placenta Amnion
49	chr11:74108600-74110400	Active TSS	Right Ventricle	heart
50	chr11:74108600-74110400	Active TSS	Small Intestine	intestine

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