Variant report

Variant	rs3136279
Chromosome Location	chr2:48017768-48017769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48013018..48016361-chr2:48016765..48019577,4	K562	blood:
2	chr2:48008394..48011813-chr2:48016879..48019860,3	K562	blood:
3	chr2:48016706..48019633-chr2:48029423..48031526,2	K562	blood:
4	chr2:48016148..48017945-chr2:48020322..48022937,3	K562	blood:

Variant related genes	Relation type
ENSG00000251872	Chromatin interaction
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 17 )
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	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136235	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136240	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136241	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136247	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136249	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136269	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136283	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3136284	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136288	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136315	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55927047	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3136279	MSH6	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48011800-48023000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:48012000-48018000	Weak transcription	Psoas Muscle	Psoas
4	chr2:48012000-48018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:48012000-48019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
9	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
11	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:48012000-48024800	Weak transcription	NHEK	skin
13	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
14	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:48012000-48026200	Weak transcription	Gastric	stomach
16	chr2:48012200-48018200	Weak transcription	Spleen	Spleen
17	chr2:48012200-48019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:48012200-48021200	Weak transcription	HMEC	breast
19	chr2:48012200-48021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:48012200-48021600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:48012200-48022000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:48012200-48022200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:48012200-48022200	Weak transcription	Osteobl	bone
24	chr2:48012200-48023000	Weak transcription	NHLF	lung
25	chr2:48012200-48023600	Weak transcription	Left Ventricle	heart
26	chr2:48012200-48024600	Weak transcription	Right Ventricle	heart
27	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
28	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:48012400-48018000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:48012400-48018200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:48012400-48019400	Weak transcription	NH-A	brain
32	chr2:48012600-48023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:48012600-48023800	Weak transcription	Colonic Mucosa	Colon
34	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:48013200-48018200	Weak transcription	Adipose Nuclei	Adipose
36	chr2:48013200-48021600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:48013400-48018200	Weak transcription	Fetal Brain Female	brain
38	chr2:48013400-48018400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:48013400-48018600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:48013400-48019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:48013400-48019400	Weak transcription	Fetal Lung	lung
42	chr2:48013400-48019600	Weak transcription	Liver	Liver
43	chr2:48013400-48021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:48013400-48021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:48013400-48021400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr2:48013400-48021400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:48013400-48021600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:48013400-48022200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:48013400-48022400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:48013400-48022400	Weak transcription	NHDF-Ad	bronchial

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