Variant report

Variant	rs11133439
Chromosome Location	chr4:57254335-57254336
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	CREB1	chr4:57253013-57254392	ECC-1	luminal epithelium:	n/a	n/a
2	TBP	chr4:57252989-57254633	GM12878	blood:	n/a	n/a
3	MXI1	chr4:57253067-57254838	IMR90	lung:	n/a	n/a
4	MXI1	chr4:57253290-57254771	K562	blood:	n/a	n/a
5	POLR2A	chr4:57254296-57254812	GM12891	blood:	n/a	n/a
6	NFYB	chr4:57253239-57254510	K562	blood:	n/a	chr4:57254016-57254028 chr4:57254014-57254029
7	POLR2A	chr4:57254214-57255273	PFSK-1	brain:	n/a	n/a
8	CCNT2	chr4:57254123-57254633	K562	blood:	n/a	n/a
9	POLR2A	chr4:57252843-57257309	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr4:57253098-57255111	K562	blood:	n/a	n/a
11	POLR2A	chr4:57253046-57257192	GM12891	blood:	n/a	n/a
12	REST	chr4:57252837-57254482	H1-neurons	neurons:	n/a	chr4:57253697-57253710 chr4:57253417-57253431 chr4:57253709-57253719
13	MYC	chr4:57253085-57254910	K562	blood:	n/a	n/a
14	TEAD4	chr4:57253207-57254944	K562	blood:	n/a	n/a
15	POLR2A	chr4:57252977-57254602	MCF10A-Er-Src	breast:	n/a	n/a
16	MAFK	chr4:57253106-57254744	K562	blood:	n/a	n/a
17	POLR2A	chr4:57254317-57254380	H1-hESC	embryonic stem cell:	n/a	n/a
18	GATA1	chr4:57253159-57256476	PBDE	blood:	n/a	chr4:57253785-57253794 chr4:57255968-57255978 chr4:57256193-57256204
19	CREB1	chr4:57253006-57254730	K562	blood:	n/a	n/a
20	POLR2A	chr4:57254095-57254430	HUVEC	blood vessel:	n/a	n/a
21	TAL1	chr4:57253164-57254807	K562	blood:	n/a	n/a
22	POLR2A	chr4:57254212-57255258	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr4:57254201-57254745	K562	blood:	n/a	n/a
24	POLR2A	chr4:57252887-57254837	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:57253157-57254673	K562	blood:	n/a	n/a
26	POLR2A	chr4:57253045-57254337	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr4:57254305-57254985	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr4:57253055-57255008	HepG2	liver:	n/a	n/a
29	POLR2A	chr4:57253047-57255279	PBDE	blood:	n/a	n/a
30	SIN3A	chr4:57253184-57254413	H1-hESC	embryonic stem cell:	n/a	chr4:57253697-57253710 chr4:57253716-57253725 chr4:57253509-57253520
31	POLR2A	chr4:57253068-57254980	HL-60	blood:	n/a	n/a
32	TEAD4	chr4:57253180-57254459	K562	blood:	n/a	n/a
33	POLR2A	chr4:57253052-57254820	HepG2	liver:	n/a	n/a
34	POLR2A	chr4:57253060-57254937	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:57253030-57254913	K562	blood:	n/a	n/a
36	POLR2A	chr4:57253107-57259459	K562	blood:	n/a	n/a
37	POLR2A	chr4:57252968-57254912	GM12878	blood:	n/a	n/a
38	MYC	chr4:57253200-57254813	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr4:57253045-57254989	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:57253190-57255024	HepG2	liver:	n/a	n/a
41	ATF1	chr4:57253190-57254720	K562	blood:	n/a	n/a
42	CREB1	chr4:57252984-57254637	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:57253098-57254890	K562	blood:	n/a	n/a
44	POLR2A	chr4:57254254-57255015	K562	blood:	n/a	n/a
45	POLR2A	chr4:57253088-57255150	K562	blood:	n/a	n/a
46	MXI1	chr4:57252900-57254796	SK-N-SH	brain:	n/a	n/a
47	MAX	chr4:57253129-57254451	NB4	blood:	n/a	n/a
48	IRF1	chr4:57253096-57254377	K562	blood:	n/a	chr4:57253774-57253788 chr4:57254230-57254240 chr4:57253773-57253785 chr4:57253770-57253784 chr4:57253773-57253786 chr4:57253774-57253784
49	POLR2A	chr4:57253088-57254878	K562	blood:	n/a	n/a
50	POLR2A	chr4:57254288-57254722	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
2	chr4:57252130..57255932-chr4:57332416..57336369,6	K562	blood:
3	chr4:57251780..57255283-chr4:57300557..57304376,5	MCF-7	breast:
4	chr4:57250870..57256510-chr4:57298204..57303491,14	K562	blood:
5	chr4:57252113..57256281-chr4:57265528..57268374,5	MCF-7	breast:
6	chr4:57251940..57255035-chr4:57332077..57334754,4	MCF-7	breast:
7	chr4:57252573..57255971-chr4:57298663..57303783,6	MCF-7	breast:
8	chr4:56813904..56818311-chr4:57252529..57254894,5	K562	blood:
9	chr4:57252189..57254981-chr4:57775973..57777493,2	MCF-7	breast:
10	chr1:43832485..43833391-chr4:57253954..57254494,2	Hela-S3	cervix:
11	chr4:57250870..57256080-chr4:57298204..57304153,16	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAICS-3	chr4:57253640-57259528	NONHSAT096500

Variant related genes	Relation type
AASDH	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000174780	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000174799	Chromatin interaction
ENSG00000066322	Chromatin interaction
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10031012	0.91[ASN][1000 genomes]
rs11133438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610	0.91[JPT][hapmap]
rs11724302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11733474	1.00[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12646703	0.95[JPT][hapmap]
rs13114104	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs13133016	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138648	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141793	0.81[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13147824	0.87[CEU][hapmap];0.84[YRI][hapmap]
rs13147900	0.91[CEU][hapmap]
rs1356787	0.91[JPT][hapmap]
rs1401904	0.91[CEU][hapmap];0.85[MEX][hapmap]
rs1401906	0.90[CEU][hapmap]
rs1401912	0.87[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1464286	0.81[EUR][1000 genomes]
rs1976815	0.81[EUR][1000 genomes]
rs1996650	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2030362	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030365	0.81[EUR][1000 genomes]
rs2139512	0.87[CEU][hapmap]
rs2292985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2899063	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs3796542	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4167	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs4864578	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4864581	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4865090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865100	0.80[EUR][1000 genomes]
rs4865101	0.81[EUR][1000 genomes]
rs6554345	0.96[CEU][hapmap]
rs6554348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554349	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6554355	0.87[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6554356	0.87[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6584	0.91[JPT][hapmap]
rs6812041	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6816268	0.91[JPT][hapmap]
rs6826795	0.82[CEU][hapmap];0.88[TSI][hapmap]
rs6830518	0.91[JPT][hapmap]
rs6834736	0.83[ASW][hapmap];0.96[CEU][hapmap];0.90[MEX][hapmap]
rs6836864	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848187	0.91[JPT][hapmap]
rs6856845	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657711	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7661712	0.81[EUR][1000 genomes]
rs7683781	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs7689163	0.87[JPT][hapmap]
rs7692385	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693137	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693683	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9312673	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9683679	0.87[CEU][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9684298	0.87[CEU][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9762333	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9997639	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11133439	AASDH	cis	multi-tissue	Pritchard
rs11133439	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs11133439	AASDH	Cis_1M	lymphoblastoid	RTeQTL
rs11133439	AASDH	cis	parietal	SCAN
rs11133439	AASDH	cis	cerebellum	SCAN
rs11133439	PPAT	cis	uninvolved skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57251800-57254400	Active TSS	Hela-S3	cervix
2	chr4:57252200-57254400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr4:57252200-57254600	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr4:57252200-57255000	Active TSS	NHLF	lung
5	chr4:57252200-57255200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:57252200-57255200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:57252200-57255200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:57252400-57254400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:57252400-57254400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:57252400-57254400	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:57252400-57254400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr4:57252400-57254400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:57252400-57254400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:57252400-57254400	Active TSS	Fetal Intestine Small	intestine
15	chr4:57252400-57254400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr4:57252400-57254400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr4:57252400-57254400	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:57252400-57254400	Active TSS	HSMM	muscle
19	chr4:57252400-57254400	Active TSS	NH-A	brain
20	chr4:57252400-57254600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:57252400-57255000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr4:57252400-57255000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:57252400-57255000	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr4:57252400-57255000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:57252400-57255200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr4:57252400-57255400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:57252400-57255600	Active TSS	K562	blood
28	chr4:57252600-57254400	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:57252600-57254400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:57252600-57254400	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr4:57252600-57254400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:57252600-57254400	Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:57252600-57254400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:57252600-57254400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:57252600-57254400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:57252600-57254400	Active TSS	Brain Angular Gyrus	brain
37	chr4:57252600-57254400	Active TSS	Brain Anterior Caudate	brain
38	chr4:57252600-57254400	Active TSS	Brain Cingulate Gyrus	brain
39	chr4:57252600-57254400	Active TSS	Brain Hippocampus Middle	brain
40	chr4:57252600-57254400	Active TSS	Brain Substantia Nigra	brain
41	chr4:57252600-57254400	Active TSS	Colon Smooth Muscle	Colon
42	chr4:57252600-57254400	Active TSS	Fetal Intestine Large	intestine
43	chr4:57252600-57254400	Active TSS	Fetal Kidney	kidney
44	chr4:57252600-57254400	Active TSS	Fetal Lung	lung
45	chr4:57252600-57254400	Active TSS	Pancreas	Pancrea
46	chr4:57252600-57254400	Active TSS	NHEK	skin
47	chr4:57252600-57254400	Active TSS	Osteobl	bone
48	chr4:57252600-57254600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:57252600-57254600	Active TSS	Colonic Mucosa	Colon
50	chr4:57252600-57254600	Active TSS	Fetal Brain Female	brain

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