Variant report

Variant	rs4488226
Chromosome Location	chr11:71164965-71164966
allele	A/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	ELF1	chr11:71163670-71164989	GM12878	blood:	n/a	chr11:71164249-71164260
2	MAZ	chr11:71163499-71165164	IMR90	lung:	n/a	chr11:71163738-71163749 chr11:71163735-71163750 chr11:71164231-71164241
3	POLR2A	chr11:71163389-71165057	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:71163492-71164976	K562	blood:	n/a	n/a
5	SIN3AK20	chr11:71162796-71165203	MCF-7	breast:	n/a	n/a
6	BHLHE40	chr11:71164289-71165095	K562	blood:	n/a	n/a
7	MAX	chr11:71162897-71165124	NB4	blood:	n/a	chr11:71163738-71163749 chr11:71163735-71163750 chr11:71164231-71164241
8	MXI1	chr11:71163613-71165127	IMR90	lung:	n/a	n/a
9	MYC	chr11:71162882-71165076	NB4	blood:	n/a	chr11:71163738-71163749 chr11:71163735-71163750 chr11:71164231-71164241
10	RCOR1	chr11:71163846-71165021	K562	blood:	n/a	n/a
11	ESR1	chr11:71164790-71165181	ECC-1	luminal epithelium:	n/a	n/a
12	ELF1	chr11:71163888-71165107	MCF-7	breast:	n/a	chr11:71164249-71164260
13	MYC	chr11:71163077-71165052	K562	blood:	n/a	chr11:71163738-71163749 chr11:71163735-71163750 chr11:71164231-71164241
14	MAX	chr11:71163355-71164992	K562	blood:	n/a	chr11:71163738-71163749 chr11:71163735-71163750 chr11:71164231-71164241
15	BHLHE40	chr11:71163260-71165062	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:
2	chr11:70652696..70654215-chr11:71163128..71165343,2	MCF-7	breast:
3	chr11:71162324..71166430-chr11:71186520..71190924,4	K562	blood:
4	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
5	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
6	chr11:71163473..71165824-chr11:71289975..71292795,2	MCF-7	breast:

Variant related genes	Relation type
NADSYN1	TF binding region
DHCR7	TF binding region
ENSG00000162105	Chromatin interaction
ENSG00000172893	Chromatin interaction
ENSG00000172890	Chromatin interaction
ENSG00000254682	Chromatin interaction
ENSG00000204572	Chromatin interaction
ENSG00000249387	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044482	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600569	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603330	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606631	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419334	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422045	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790010	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792306	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.80[ASN][1000 genomes]
rs12806844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807718	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981412	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040323	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276361	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276362	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852853	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750997	0.89[EUR][1000 genomes]
rs3794060	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944062	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944949	0.93[ASN][1000 genomes]
rs4944955	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944956	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944958	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944996	0.89[ASN][1000 genomes]
rs4945008	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928249	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909217	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4488226	RP11-660L16.2	cis	lung	GTEx
rs4488226	NADSYN1	cis	Nerve Tibial	GTEx
rs4488226	NADSYN1	cis	lung	GTEx
rs4488226	RP11-660L16.2	cis	Artery Aorta	GTEx
rs4488226	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs4488226	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4488226	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs4488226	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs4488226	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs4488226	NADSYN1	cis	Thyroid	GTEx
rs4488226	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs4488226	RP11-660L16.2	cis	Whole Blood	GTEx
rs4488226	RP11-660L16.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71162600-71165400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:71163000-71165000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:71163000-71165000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:71163000-71165000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:71163000-71165200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:71163000-71165200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr11:71163000-71165200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr11:71163000-71165200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:71163000-71165800	Active TSS	Rectal Smooth Muscle	rectum
10	chr11:71163200-71165000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:71163200-71165000	Active TSS	Brain Substantia Nigra	brain
12	chr11:71163200-71165000	Active TSS	Psoas Muscle	Psoas
13	chr11:71163200-71165000	Active TSS	Right Atrium	heart
14	chr11:71163200-71165200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:71163200-71165400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:71163400-71165000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:71163400-71165000	Active TSS	Fetal Kidney	kidney
18	chr11:71163400-71165200	Active TSS	Esophagus	oesophagus
19	chr11:71163400-71165200	Active TSS	Ovary	ovary
20	chr11:71163400-71165200	Active TSS	Stomach Mucosa	stomach
21	chr11:71163400-71165400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:71163400-71165400	Active TSS	HSMMtube	muscle
23	chr11:71163600-71165000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr11:71163600-71165200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr11:71163600-71165200	Active TSS	Aorta	Aorta
26	chr11:71163600-71165200	Active TSS	Small Intestine	intestine
27	chr11:71163800-71165000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:71163800-71165000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:71163800-71165000	Active TSS	Muscle Satellite Cultured Cells	--
30	chr11:71163800-71165000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:71163800-71165000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr11:71163800-71165000	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr11:71163800-71165000	Active TSS	A549	lung
34	chr11:71163800-71165200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:71163800-71165200	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr11:71163800-71165200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr11:71163800-71165200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:71163800-71165200	Active TSS	GM12878-XiMat	blood
39	chr11:71163800-71165400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:71163800-71165400	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr11:71163800-71165400	Active TSS	NHDF-Ad	bronchial
42	chr11:71164000-71165000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:71164000-71165000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:71164000-71165000	Bivalent/Poised TSS	HepG2	liver
45	chr11:71164000-71165000	Active TSS	HMEC	breast
46	chr11:71164000-71165000	Active TSS	K562	blood
47	chr11:71164000-71165000	Active TSS	NH-A	brain
48	chr11:71164000-71165400	Active TSS	NHLF	lung
49	chr11:71164000-71165800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:71164400-71165000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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