Variant report

Variant	rs2088100
Chromosome Location	chr1:45877575-45877576
allele	C/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	GATA3	chr1:45877093-45877659	T-47D	breast:	n/a	n/a
2	GTF2F1	chr1:45877409-45877583	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr1:45877135-45877651	T-47D	breast:	n/a	n/a
4	CTCF	chr1:45877540-45877690	NHEK	skin:	n/a	n/a
5	GATA3	chr1:45876278-45877696	MCF-7	breast:	n/a	n/a
6	GATA3	chr1:45876280-45877621	MCF-7	breast:	n/a	n/a
7	JUN	chr1:45876543-45878303	K562	blood:	n/a	n/a
8	SIN3AK20	chr1:45876416-45877695	MCF-7	breast:	n/a	n/a
9	ZNF217	chr1:45876625-45877696	MCF-7	breast:	n/a	n/a
10	GATA3	chr1:45876576-45877654	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45806484..45809522-chr1:45876686..45880375,3	K562	blood:

Variant related genes	Relation type
ENSG00000236872	TF binding region
ENSG00000132773	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1006216	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1007858	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10789464	0.83[EUR][1000 genomes]
rs1084166	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10890327	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890330	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211101	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211108	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211111	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211117	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211118	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211123	0.83[EUR][1000 genomes]
rs11211124	0.83[EUR][1000 genomes]
rs12029322	0.83[EUR][1000 genomes]
rs12037201	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12037411	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042903	0.81[EUR][1000 genomes]
rs12046816	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067642	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12097497	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12410493	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12564806	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1417578	0.89[EUR][1000 genomes]
rs1494812	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17395553	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771551	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1826691	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2050884	0.89[EUR][1000 genomes]
rs2055145	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153607	0.85[EUR][1000 genomes]
rs2153608	0.85[EUR][1000 genomes]
rs2153609	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2185549	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298018	0.85[EUR][1000 genomes]
rs2487442	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2492836	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2492840	0.89[EUR][1000 genomes]
rs28555082	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3219463	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3219472	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3219489	0.83[EUR][1000 genomes]
rs3790582	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3790583	0.83[EUR][1000 genomes]
rs4660301	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660849	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660851	0.90[EUR][1000 genomes]
rs4660852	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660853	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660854	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4660855	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660858	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4660863	0.83[EUR][1000 genomes]
rs55642258	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61788261	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61788262	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61788281	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61788285	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61791362	0.85[EUR][1000 genomes]
rs61791368	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61791369	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72686460	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7417107	0.89[EUR][1000 genomes]
rs7525849	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7528573	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7531253	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532762	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7536135	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7543428	0.90[EUR][1000 genomes]
rs7544178	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553318	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs781226	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs781230	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs781232	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs884962	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9326141	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429072	0.85[EUR][1000 genomes]
rs9429073	0.80[EUR][1000 genomes]
rs9429074	0.85[EUR][1000 genomes]
rs9429076	0.86[EUR][1000 genomes]
rs9429158	0.87[EUR][1000 genomes]
rs9429159	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429160	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429161	0.90[EUR][1000 genomes]
rs9729395	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2088100	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs2088100	MMACHC	cis	multi-tissue	Pritchard
rs2088100	C2orf49	trans	lymphoblastoid	RTeQTL
rs2088100	TESK2	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45869400-45885400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:45875600-45878600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:45875600-45889400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:45876600-45877600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:45876600-45877600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:45876600-45877600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:45876600-45878400	Enhancers	K562	blood
9	chr1:45876600-45880000	Enhancers	Primary B cells from cord blood	blood
10	chr1:45876600-45880400	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:45876600-45881600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:45876800-45877800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:45876800-45879200	Enhancers	GM12878-XiMat	blood
14	chr1:45876800-45887800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:45877000-45877600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:45877000-45877600	Enhancers	Placenta	Placenta
17	chr1:45877000-45877600	Enhancers	Gastric	stomach
18	chr1:45877000-45877600	Enhancers	Spleen	Spleen
19	chr1:45877000-45878600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:45877000-45886800	Weak transcription	Liver	Liver
21	chr1:45877200-45877600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:45877200-45877600	Enhancers	Esophagus	oesophagus
23	chr1:45877200-45877800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:45877200-45887800	Weak transcription	Fetal Intestine Large	intestine
25	chr1:45877200-45888200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:45877400-45877600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:45877400-45877800	Enhancers	NHEK	skin
28	chr1:45877400-45878200	Enhancers	Hela-S3	cervix
29	chr1:45877400-45886800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:45877400-45889200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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