Variant report

Variant	rs2001732
Chromosome Location	chr3:52880740-52880741
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	EBF1	chr3:52880648-52880901	GM12878	blood:	n/a	n/a
2	BHLHE40	chr3:52880598-52880906	GM12878	blood:	n/a	n/a
3	MAX	chr3:52880735-52880927	GM12878	blood:	n/a	chr3:52880799-52880808
4	EBF1	chr3:52880587-52880919	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52873625..52875144-chr3:52879185..52881871,2	K562	blood:

Variant related genes	Relation type
TMEM110-MUSTN1	TF binding region
TMEM110	TF binding region
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10510761	0.87[GIH][hapmap]
rs11130329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1139106	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707829	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs11708337	0.85[CEU][hapmap]
rs11708390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11709430	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11710394	0.87[GIH][hapmap]
rs11712498	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11713324	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs11714793	0.85[CEU][hapmap]
rs11715498	0.91[CEU][hapmap]
rs11717619	0.87[GIH][hapmap]
rs11717749	1.00[CHB][hapmap]
rs11718060	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720228	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11720233	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13067373	0.93[CEU][hapmap]
rs13076033	1.00[CHB][hapmap]
rs13080929	0.87[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095705	0.85[CEU][hapmap]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	0.93[CEU][hapmap]
rs2071039	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2240916	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276818	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276822	1.00[JPT][hapmap]
rs2336661	0.93[CEU][hapmap]
rs28552648	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs33999310	1.00[ASN][1000 genomes]
rs34288509	1.00[ASN][1000 genomes]
rs34860124	1.00[ASN][1000 genomes]
rs3733035	0.85[CEU][hapmap]
rs3755801	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3755805	0.92[ASN][1000 genomes]
rs3796352	1.00[CHB][hapmap]
rs4687556	0.81[EUR][1000 genomes]
rs4687676	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798472	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs9637477	0.82[EUR][1000 genomes]
rs9831977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2001732	TMEM110	Cis_1M	lymphoblastoid	RTeQTL
rs2001732	TMEM110	cis	multi-tissue	Pritchard
rs2001732	TMEM110	cis	Thyroid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52866000-52884800	Weak transcription	HMEC	breast
4	chr3:52866200-52885200	Weak transcription	NHEK	skin
5	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
9	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
13	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
14	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52873600-52881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52873600-52882600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:52873600-52889000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:52873800-52882200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:52873800-52889000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:52874200-52883800	Enhancers	Psoas Muscle	Psoas
22	chr3:52875800-52882600	Weak transcription	NH-A	brain
23	chr3:52875800-52885800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:52876000-52885800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:52876600-52881200	Weak transcription	Fetal Intestine Large	intestine
26	chr3:52876800-52881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:52876800-52881600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:52876800-52881600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52876800-52881600	Weak transcription	Dnd41	blood
30	chr3:52876800-52882000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:52876800-52883600	Weak transcription	Aorta	Aorta
32	chr3:52877000-52881200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:52877000-52881200	Weak transcription	Ovary	ovary
34	chr3:52877000-52881800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:52877000-52882200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:52877000-52883200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:52877000-52885000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:52877000-52885600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:52877200-52881000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:52877200-52882200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:52877400-52881200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:52877400-52881600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:52877800-52881000	Weak transcription	Brain Germinal Matrix	brain
44	chr3:52877800-52881400	Weak transcription	Gastric	stomach
45	chr3:52877800-52881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:52878000-52881200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:52878000-52881200	Weak transcription	Spleen	Spleen
48	chr3:52878200-52880800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:52878200-52880800	Enhancers	Brain Cingulate Gyrus	brain
50	chr3:52878200-52881000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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