Variant report

Variant	rs3136240
Chromosome Location	chr2:48012086-48012087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48008927..48012318-chr2:48131369..48134669,5	MCF-7	breast:
2	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
3	chr2:48011141..48015679-chr2:48023292..48025475,4	MCF-7	breast:
4	chr2:48010207..48012260-chr2:48541505..48544232,2	K562	blood:

Variant related genes	Relation type
ENSG00000138081	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000235369	Chromatin interaction
ENSG00000170802	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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1800932	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136235	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3136241	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136247	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136249	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136269	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136279	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136283	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136284	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136288	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136315	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55927047	0.95[AMR][1000 genomes];0.95[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
rs3136240	MSH6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48009000-48012400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:48009200-48012200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:48009200-48012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:48009200-48012600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:48009200-48012800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:48009200-48012800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:48009400-48012200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:48009400-48012200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:48009400-48012200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:48009400-48012200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr2:48009400-48012200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:48009400-48012200	Active TSS	Colonic Mucosa	Colon
13	chr2:48009400-48012200	Active TSS	NHLF	lung
14	chr2:48009400-48012400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:48009400-48012400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:48009400-48012600	Active TSS	HSMM	muscle
17	chr2:48009400-48012800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:48009400-48013400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:48009400-48013400	Active TSS	Ovary	ovary
20	chr2:48009600-48012200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:48009600-48012200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:48009600-48012200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:48009600-48012400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:48009600-48012400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:48009600-48012400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:48009800-48012200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:48010000-48012200	Active TSS	HMEC	breast
28	chr2:48010000-48013400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48011200-48012200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:48011200-48012400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr2:48011400-48012200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr2:48011400-48012200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:48011400-48012200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:48011400-48012200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr2:48011400-48012200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr2:48011400-48012200	Enhancers	Spleen	Spleen
37	chr2:48011400-48012200	Flanking Active TSS	HUVEC	blood vessel
38	chr2:48011400-48012400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:48011400-48015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:48011600-48012200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:48011600-48012200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:48011600-48012200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:48011600-48012200	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr2:48011600-48012200	Enhancers	Small Intestine	intestine
45	chr2:48011600-48012600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
46	chr2:48011600-48013400	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr2:48011600-48013400	Enhancers	Fetal Brain Male	brain
48	chr2:48011600-48014200	Enhancers	Primary B cells from peripheral blood	blood
49	chr2:48011600-48014200	Transcr. at gene 5' and 3'	Dnd41	blood
50	chr2:48011800-48012200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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