Variant report

Variant	rs55927047
Chromosome Location	chr2:48010654-48010655
allele	C/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	TBP	chr2:48009724-48011312	H1-hESC	embryonic stem cell:	n/a	n/a
2	BCL3	chr2:48009938-48010674	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr2:48009451-48011776	MCF-7	breast:	n/a	n/a
4	MAX	chr2:48009528-48011580	NB4	blood:	n/a	chr2:48011032-48011042
5	POLR2A	chr2:48009627-48011001	HL-60	blood:	n/a	n/a
6	CCNT2	chr2:48009723-48011419	K562	blood:	n/a	chr2:48011044-48011053 chr2:48010131-48010140 chr2:48010643-48010652 chr2:48010993-48011002 chr2:48010712-48010721
7	POLR2A	chr2:48009642-48010925	U87	brain:	n/a	n/a
8	POLR2A	chr2:48009488-48011430	HepG2	liver:	n/a	n/a
9	MAX	chr2:48009727-48010893	HepG2	liver:	n/a	n/a
10	MYC	chr2:48010039-48010716	H1-hESC	embryonic stem cell:	n/a	n/a
11	BCL3	chr2:48010143-48010771	A549	lung:	n/a	chr2:48010665-48010678
12	BHLHE40	chr2:48009535-48010884	K562	blood:	n/a	n/a
13	CHD2	chr2:48009671-48010970	HepG2	liver:	n/a	chr2:48010273-48010283
14	MYC	chr2:48009537-48011035	A549	lung:	n/a	n/a
15	POLR2A	chr2:48009321-48010999	Hela-S3	cervix:	n/a	n/a
16	EBF1	chr2:48009863-48010672	GM12878	blood:	n/a	n/a
17	EP300	chr2:48009619-48010969	ECC-1	luminal epithelium:	n/a	n/a
18	BCLAF1	chr2:48009585-48010673	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:48009627-48011455	K562	blood:	n/a	n/a
20	E2F6	chr2:48009686-48011751	A549	lung:	n/a	chr2:48010286-48010295 chr2:48011052-48011064 chr2:48010287-48010294 chr2:48010235-48010244 chr2:48010287-48010294 chr2:48009932-48009941 chr2:48011044-48011053 chr2:48010285-48010296 chr2:48010286-48010294 chr2:48010750-48010759 chr2:48010286-48010298 chr2:48010287-48010294 chr2:48011131-48011140
21	POLR2A	chr2:48009691-48011296	GM18526	blood:	n/a	n/a
22	MAX	chr2:48009393-48010957	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr2:48009858-48011415	MCF-7	breast:	n/a	n/a
24	POLR2A	chr2:48009667-48011276	HepG2	liver:	n/a	n/a
25	MAX	chr2:48009757-48011049	H1-hESC	embryonic stem cell:	n/a	chr2:48011032-48011042
26	POLR2A	chr2:48009704-48011601	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr2:48009620-48011271	GM18505	blood:	n/a	n/a
28	POLR2A	chr2:48009647-48011413	K562	blood:	n/a	n/a
29	MAX	chr2:48009771-48011556	K562	blood:	n/a	chr2:48011032-48011042
30	REST	chr2:48009460-48011268	H1-neurons	neurons:	n/a	chr2:48010029-48010042
31	MAX	chr2:48009728-48010708	K562	blood:	n/a	n/a
32	RCOR1	chr2:48009401-48010939	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr2:48010580-48010730	Caco-2	colon:	n/a	n/a
34	SIN3A	chr2:48009977-48011336	GM12878	blood:	n/a	chr2:48010670-48010681 chr2:48010096-48010107 chr2:48010029-48010042 chr2:48010262-48010273
35	TAF1	chr2:48010160-48010985	A549	lung:	n/a	n/a
36	TCF12	chr2:48009723-48010759	ECC-1	luminal epithelium:	n/a	n/a
37	FOXA2	chr2:48009943-48010985	A549	lung:	n/a	n/a
38	E2F6	chr2:48009873-48010662	K562	blood:	n/a	chr2:48010286-48010295 chr2:48010287-48010294 chr2:48010235-48010244 chr2:48010287-48010294 chr2:48009932-48009941 chr2:48010285-48010296 chr2:48010286-48010294 chr2:48010286-48010298 chr2:48010287-48010294
39	POLR2A	chr2:48009547-48011872	Hela-S3	cervix:	n/a	n/a
40	MAX	chr2:48009787-48010726	MCF-7	breast:	n/a	n/a
41	HCFC1	chr2:48009441-48011000	Hela-S3	cervix:	n/a	n/a
42	MAX	chr2:48009475-48011647	HepG2	liver:	n/a	chr2:48011032-48011042
43	E2F4	chr2:48009800-48011318	K562	blood:	n/a	chr2:48010286-48010295 chr2:48011052-48011064 chr2:48010287-48010294 chr2:48010235-48010244 chr2:48010287-48010294 chr2:48009932-48009941 chr2:48011044-48011053 chr2:48010286-48010294 chr2:48010750-48010759 chr2:48010286-48010298 chr2:48010287-48010294 chr2:48010285-48010296 chr2:48011131-48011140
44	CTCF	chr2:48010653-48011073	K562	blood:	n/a	chr2:48010911-48010924
45	PBX3	chr2:48010652-48011385	A549	lung:	n/a	n/a
46	FOXA2	chr2:48010634-48011036	A549	lung:	n/a	n/a
47	POLR2A	chr2:48009863-48011366	HEK293	kidney:	n/a	n/a
48	POLR2A	chr2:48010639-48010980	ECC-1	luminal epithelium:	n/a	n/a
49	MYC	chr2:48009642-48011549	K562	blood:	n/a	chr2:48011032-48011042
50	ZBTB7A	chr2:48009659-48011512	ECC-1	luminal epithelium:	n/a	chr2:48010938-48010945

No.	Distal block	Cell Line	Cell type
1	chr2:48009860..48010854-chr5:108745171..108745972,2	Hela-S3	cervix:
2	chr17:62501791..62502687-chr2:48009810..48010670,2	Hela-S3	cervix:
3	chr2:48008927..48012318-chr2:48131369..48134669,5	MCF-7	breast:
4	chr2:47629900..47631449-chr2:48009384..48011204,2	K562	blood:
5	chr2:47403115..47403699-chr2:48010169..48010689,2	Hela-S3	cervix:
6	chr2:48009680..48011593-chr2:48034365..48037361,4	K562	blood:
7	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
8	chr2:48009330..48011315-chr2:48667151..48669363,2	MCF-7	breast:
9	chr2:47400478..47403818-chr2:48008752..48011597,4	K562	blood:
10	chr2:48009081..48011260-chr2:48666512..48669305,2	K562	blood:
11	chr2:48009241..48011521-chr2:48133698..48136009,2	K562	blood:
12	chr2:48010056..48010954-chr3:52570382..52571267,2	Hela-S3	cervix:
13	chr2:48009564..48012056-chr2:48131613..48133953,3	MCF-7	breast:
14	chr2:48010207..48012260-chr2:48541505..48544232,2	K562	blood:

Variant related genes	Relation type
MSH6	TF binding region
ENSG00000162869	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000198961	Chromatin interaction
ENSG00000138081	Chromatin interaction
ENSG00000235369	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1042820	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1800932	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136235	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136240	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136241	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136247	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136249	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136269	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136279	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3136283	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3136284	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136288	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3136315	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv873999	chr2:47916074-48019485	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
3	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3392564	chr2:48009598-48012596	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55927047	MSH6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48008400-48011400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:48009000-48011400	Active TSS	Rectal Smooth Muscle	rectum
3	chr2:48009000-48012400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:48009200-48012000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:48009200-48012200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:48009200-48012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:48009200-48012600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:48009200-48012800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:48009200-48012800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:48009400-48011000	Bivalent/Poised TSS	HepG2	liver
11	chr2:48009400-48011400	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr2:48009400-48011400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:48009400-48011400	Active TSS	Stomach Smooth Muscle	stomach
14	chr2:48009400-48011600	Active TSS	Brain Anterior Caudate	brain
15	chr2:48009400-48011600	Active TSS	Brain Substantia Nigra	brain
16	chr2:48009400-48011600	Active TSS	Left Ventricle	heart
17	chr2:48009400-48011600	Active TSS	Pancreas	Pancrea
18	chr2:48009400-48011600	Active TSS	Psoas Muscle	Psoas
19	chr2:48009400-48011600	Active TSS	Right Ventricle	heart
20	chr2:48009400-48011600	Active TSS	Stomach Mucosa	stomach
21	chr2:48009400-48011600	Active TSS	NHEK	skin
22	chr2:48009400-48011800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:48009400-48011800	Active TSS	Brain Germinal Matrix	brain
24	chr2:48009400-48011800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:48009400-48011800	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr2:48009400-48011800	Active TSS	Fetal Brain Female	brain
27	chr2:48009400-48011800	Active TSS	Fetal Lung	lung
28	chr2:48009400-48011800	Active TSS	Fetal Stomach	stomach
29	chr2:48009400-48011800	Active TSS	A549	lung
30	chr2:48009400-48012000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:48009400-48012000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:48009400-48012000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:48009400-48012000	Active TSS	Brain Angular Gyrus	brain
34	chr2:48009400-48012000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:48009400-48012000	Active TSS	Right Atrium	heart
36	chr2:48009400-48012000	Active TSS	NHDF-Ad	bronchial
37	chr2:48009400-48012200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr2:48009400-48012200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr2:48009400-48012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:48009400-48012200	Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:48009400-48012200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:48009400-48012200	Active TSS	Colonic Mucosa	Colon
43	chr2:48009400-48012200	Active TSS	NHLF	lung
44	chr2:48009400-48012400	Active TSS	H1 Cell Line	embryonic stem cell
45	chr2:48009400-48012400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:48009400-48012600	Active TSS	HSMM	muscle
47	chr2:48009400-48012800	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr2:48009400-48013400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:48009400-48013400	Active TSS	Ovary	ovary
50	chr2:48009600-48010800	Active TSS	Primary T killer memory cells from peripheral blood	blood

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