Variant report

Variant	rs11235809
Chromosome Location	chr11:73290163-73290164
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	ELF1	chr11:73289902-73290190	K562	blood:	n/a	chr11:73290065-73290078
2	ATF2	chr11:73289691-73290216	GM12878	blood:	n/a	n/a
3	BATF	chr11:73289721-73290174	GM12878	blood:	n/a	n/a
4	SPI1	chr11:73289847-73290361	HL-60	blood:	n/a	n/a
5	GATA3	chr11:73289632-73290240	SK-N-SH	brain:	n/a	n/a
6	FOXA1	chr11:73289675-73290238	HepG2	liver:	n/a	n/a
7	ATF2	chr11:73289783-73290212	GM12878	blood:	n/a	n/a
8	SETDB1	chr11:73289734-73290299	U2OS	brain:	n/a	n/a
9	BCLAF1	chr11:73289736-73290299	GM12878	blood:	n/a	n/a
10	RUNX3	chr11:73289392-73290344	GM12878	blood:	n/a	n/a
11	SPI1	chr11:73289885-73290229	GM12891	blood:	n/a	n/a
12	GATA3	chr11:73289756-73290209	MCF-7	breast:	n/a	n/a
13	FOXA1	chr11:73289818-73290257	HepG2	liver:	n/a	n/a
14	SPI1	chr11:73289808-73290327	GM12878	blood:	n/a	n/a
15	SPI1	chr11:73290016-73290164	GM12878	blood:	n/a	n/a
16	MEF2A	chr11:73289727-73290253	GM12878	blood:	n/a	n/a
17	GATA3	chr11:73289710-73290243	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr11:73289407-73290215	GM12878	blood:	n/a	n/a
19	ZNF143	chr11:73289945-73290165	GM12878	blood:	n/a	n/a
20	SPI1	chr11:73289921-73290225	GM12878	blood:	n/a	n/a
21	SPI1	chr11:73289882-73290285	GM12891	blood:	n/a	n/a
22	ELF1	chr11:73289968-73290242	HepG2	liver:	n/a	chr11:73290065-73290078
23	PBX3	chr11:73289673-73290184	SK-N-SH	brain:	n/a	n/a
24	RUNX3	chr11:73289757-73290270	GM12878	blood:	n/a	n/a
25	BHLHE40	chr11:73289897-73290217	GM12878	blood:	n/a	n/a
26	ELF1	chr11:73289841-73290275	GM12878	blood:	n/a	chr11:73290065-73290078

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73289699..73292318-chr11:73308150..73310462,2	K562	blood:

Variant related genes	Relation type
HMGN2P38	TF binding region
ENSG00000054965	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1002126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1002127	1.00[CEU][hapmap]
rs10501411	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11235738	1.00[JPT][hapmap]
rs11235745	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11235746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11235759	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11235770	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11235775	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11820577	0.80[EUR][1000 genomes]
rs11822984	0.80[EUR][1000 genomes]
rs11823913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11826896	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11826909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12269884	1.00[JPT][hapmap]
rs12274589	1.00[JPT][hapmap]
rs12276892	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12277924	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282790	1.00[JPT][hapmap]
rs12285885	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12290623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12290701	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290785	0.80[EUR][1000 genomes]
rs12290835	1.00[JPT][hapmap]
rs17132115	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	1.00[CEU][hapmap]
rs17244602	1.00[CEU][hapmap]
rs17244616	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17310361	1.00[CEU][hapmap]
rs17310374	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17851510	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs1938777	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs2298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs3825005	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs56884659	0.80[EUR][1000 genomes]
rs57491850	0.83[EUR][1000 genomes]
rs58573166	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59806295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60860405	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61516411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7101831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7110369	0.88[CEU][hapmap]
rs7114009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs7114376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115055	1.00[CEU][hapmap]
rs7118982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes]
rs7123985	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7129990	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs7131397	1.00[JPT][hapmap]
rs724111	1.00[CEU][hapmap]
rs73546720	0.80[EUR][1000 genomes]
rs73546735	0.80[EUR][1000 genomes]
rs73548680	0.80[EUR][1000 genomes]
rs73548688	0.80[EUR][1000 genomes]
rs73548693	0.83[EUR][1000 genomes]
rs73550316	0.83[EUR][1000 genomes]
rs7925226	1.00[CEU][hapmap]
rs7927344	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934218	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938391	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7941359	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs7944346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945825	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7950375	0.80[EUR][1000 genomes]
rs7951072	1.00[CEU][hapmap]
rs7952686	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs880317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9888218	1.00[JPT][hapmap]

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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv983188	chr11:73273934-73307064	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	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
5	nsv975202	chr11:73289057-73294849	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11235809	ARHGEF17	cis	Whole Blood	GTEx
rs11235809	CCND1	cis	cerebellum	SCAN
rs11235809	P2RY2	cis	cerebellum	SCAN
rs11235809	FAM168A	cis	Whole Blood	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73250000-73307800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:73253800-73307000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:73263200-73306000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:73266600-73307800	Weak transcription	Fetal Intestine Small	intestine
5	chr11:73272200-73307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:73274800-73290800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr11:73275400-73307000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:73276400-73296800	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:73276400-73299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:73276400-73307000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:73277200-73299600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:73277400-73307800	Weak transcription	Fetal Intestine Large	intestine
13	chr11:73277600-73293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:73279400-73307000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:73279600-73291200	Weak transcription	Ovary	ovary
16	chr11:73280000-73299400	Weak transcription	Fetal Stomach	stomach
17	chr11:73280600-73296200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:73281600-73307800	Weak transcription	Hela-S3	cervix
19	chr11:73281800-73295400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr11:73282000-73296800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:73282200-73296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:73282200-73296600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:73282200-73297000	Weak transcription	HMEC	breast
24	chr11:73282200-73297200	Weak transcription	NH-A	brain
25	chr11:73282400-73293800	Weak transcription	HSMM	muscle
26	chr11:73285200-73292400	Weak transcription	Right Atrium	heart
27	chr11:73285200-73294600	Weak transcription	Right Ventricle	heart
28	chr11:73285200-73303600	Weak transcription	Left Ventricle	heart
29	chr11:73285200-73306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:73286000-73294800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:73286200-73295000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:73286800-73290200	Enhancers	Brain Germinal Matrix	brain
33	chr11:73286800-73307600	Weak transcription	Lung	lung
34	chr11:73287800-73306200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:73288000-73290200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:73288000-73290200	Enhancers	NHLF	lung
37	chr11:73288000-73291200	Enhancers	Fetal Brain Male	brain
38	chr11:73288000-73306200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:73288200-73293800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:73288400-73307800	Weak transcription	Aorta	Aorta
41	chr11:73288600-73290200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:73288600-73290400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr11:73288800-73290200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr11:73288800-73290200	Enhancers	Colon Smooth Muscle	Colon
45	chr11:73288800-73290400	Enhancers	Fetal Brain Female	brain
46	chr11:73288800-73290400	Enhancers	HepG2	liver
47	chr11:73288800-73307600	Weak transcription	Fetal Kidney	kidney
48	chr11:73289000-73290200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr11:73289000-73290200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr11:73289000-73290200	Enhancers	Rectal Smooth Muscle	rectum

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