Variant report

Variant	rs11211123
Chromosome Location	chr1:45957609-45957610
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	POLR2A	chr1:45957522-45958055	HepG2	liver:	n/a	n/a
2	MXI1	chr1:45955657-45957822	SK-N-SH	brain:	n/a	n/a
3	MAFK	chr1:45957088-45957623	H1-hESC	embryonic stem cell:	n/a	chr1:45957294-45957309
4	MAZ	chr1:45955829-45958126	IMR90	lung:	n/a	chr1:45956983-45956993 chr1:45956501-45956511 chr1:45956983-45956994 chr1:45956984-45956993 chr1:45956984-45956993 chr1:45956979-45956998 chr1:45956983-45956994 chr1:45956982-45956995 chr1:45956985-45956994 chr1:45956984-45956994 chr1:45956982-45956995 chr1:45956983-45956993 chr1:45956893-45956903 chr1:45956982-45956995 chr1:45956982-45956995 chr1:45956984-45956993 chr1:45957177-45957187
5	SP1	chr1:45956503-45957637	HCT-116	colon:	n/a	chr1:45956870-45956879 chr1:45956893-45956907 chr1:45956869-45956879 chr1:45956868-45956880 chr1:45957022-45957043 chr1:45956870-45956879 chr1:45956887-45956899 chr1:45956869-45956879 chr1:45957177-45957187 chr1:45957177-45957186 chr1:45956868-45956880 chr1:45957176-45957188 chr1:45956858-45956872 chr1:45956888-45956898 chr1:45956869-45956878 chr1:45957176-45957188 chr1:45957245-45957266 chr1:45957178-45957187 chr1:45956865-45956879 chr1:45956887-45956899 chr1:45957173-45957187 chr1:45956888-45956898
6	SP1	chr1:45956431-45957689	HCT-116	colon:	n/a	chr1:45956870-45956879 chr1:45956893-45956907 chr1:45956869-45956879 chr1:45956868-45956880 chr1:45957022-45957043 chr1:45956870-45956879 chr1:45956887-45956899 chr1:45956869-45956879 chr1:45957177-45957187 chr1:45957177-45957186 chr1:45956868-45956880 chr1:45957176-45957188 chr1:45956858-45956872 chr1:45956888-45956898 chr1:45956869-45956878 chr1:45957176-45957188 chr1:45957245-45957266 chr1:45957178-45957187 chr1:45956865-45956879 chr1:45956887-45956899 chr1:45957173-45957187 chr1:45956888-45956898
7	NFYB	chr1:45956645-45957626	GM12878	blood:	n/a	chr1:45957061-45957076

No.	Distal block	Cell Line	Cell type
1	chr1:45285788..45287564-chr1:45957142..45958713,2	K562	blood:
2	chr1:45819408..45822200-chr1:45957439..45959167,2	K562	blood:
3	chr1:45954972..45958180-chr1:45986651..45988959,5	K562	blood:
4	chr1:45284051..45286963-chr1:45955416..45958247,2	MCF-7	breast:
5	chr1:45956512..45959436-chr1:45986078..45988665,3	MCF-7	breast:
6	chr1:45805035..45807382-chr1:45957250..45960213,2	MCF-7	breast:
7	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
8	chr1:45957125..45959472-chr1:46015494..46017725,2	K562	blood:

Variant related genes	Relation type
TESK2	TF binding region
ENSG00000132763	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1006216	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1007858	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890327	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890330	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211108	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211111	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211117	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211118	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211128	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12029322	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042903	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046816	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12066142	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12067642	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12097497	0.83[EUR][1000 genomes]
rs12410493	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564806	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1494812	0.83[EUR][1000 genomes]
rs1771551	0.81[EUR][1000 genomes]
rs1826691	0.82[EUR][1000 genomes]
rs2055145	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088100	0.83[EUR][1000 genomes]
rs28555082	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2883968	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34673142	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790582	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3790583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4633317	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660855	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660858	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4660863	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5015340	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55642258	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788261	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788262	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61788281	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61788285	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788336	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788356	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61791369	0.81[EUR][1000 genomes]
rs67683090	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs713358	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7528573	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7531253	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs781226	0.80[EUR][1000 genomes]
rs781230	0.81[EUR][1000 genomes]
rs781232	0.81[EUR][1000 genomes]
rs868351	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9727262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9729395	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11211123	C2orf49	trans	lymphoblastoid	RTeQTL
rs11211123	MMACHC	cis	multi-tissue	Pritchard
rs11211123	PRDX1	cis	Thyroid	GTEx
rs11211123	TESK2	cis	Whole Blood	GTEx
rs11211123	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45955800-45957800	Active TSS	Brain Substantia Nigra	brain
2	chr1:45955800-45957800	Active TSS	NHDF-Ad	bronchial
3	chr1:45956200-45957800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:45956400-45957800	Active TSS	A549	lung
5	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
8	chr1:45956800-45965000	Weak transcription	Gastric	stomach
9	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
10	chr1:45957000-45957800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:45957000-45957800	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr1:45957000-45957800	Flanking Active TSS	Dnd41	blood
13	chr1:45957000-45962600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:45957000-45964200	Weak transcription	Pancreas	Pancrea
15	chr1:45957000-45964400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:45957200-45957800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr1:45957200-45957800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:45957200-45957800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:45957200-45957800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:45957200-45957800	Flanking Active TSS	Liver	Liver
23	chr1:45957200-45958000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:45957200-45958000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:45957200-45961800	Weak transcription	Lung	lung
26	chr1:45957200-45964200	Weak transcription	K562	blood
27	chr1:45957400-45957800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:45957400-45957800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:45957400-45957800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:45957400-45957800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:45957400-45957800	Enhancers	Fetal Brain Male	brain
32	chr1:45957400-45957800	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:45957400-45957800	Enhancers	Placenta	Placenta
34	chr1:45957400-45957800	Flanking Active TSS	GM12878-XiMat	blood
35	chr1:45957400-45957800	Flanking Active TSS	Hela-S3	cervix
36	chr1:45957400-45958000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:45957400-45958000	Enhancers	Fetal Thymus	thymus
38	chr1:45957400-45959800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:45957400-45964000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:45957400-45965200	Weak transcription	HSMM	muscle
42	chr1:45957600-45957800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr1:45957600-45957800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:45957600-45957800	Enhancers	Primary hematopoietic stem cells	blood
45	chr1:45957600-45957800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:45957600-45957800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:45957600-45957800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:45957600-45957800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:45957600-45957800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:45957600-45957800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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