Variant report

Variant	rs3136269
Chromosome Location	chr2:48016353-48016354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48009604..48011785-chr2:48013652..48016498,2	K562	blood:
2	chr2:48013018..48016361-chr2:48016765..48019577,4	K562	blood:
3	chr2:48016148..48017945-chr2:48020322..48022937,3	K562	blood:

Variant related genes	Relation type
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1042820	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1800932	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136235	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3136240	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136279	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136284	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136288	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136315	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55927047	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57632619	0.93[AFR][1000 genomes]
rs58419715	0.93[AFR][1000 genomes]
rs60444285	0.93[AFR][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
rs3136269	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	chr2:48012000-48017600	Weak transcription	Fetal Kidney	kidney
4	chr2:48012000-48018000	Weak transcription	Psoas Muscle	Psoas
5	chr2:48012000-48018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:48012000-48019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
10	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
12	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:48012000-48024800	Weak transcription	NHEK	skin
14	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
15	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:48012000-48026200	Weak transcription	Gastric	stomach
17	chr2:48012200-48017400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:48012200-48017400	Weak transcription	Thymus	Thymus
19	chr2:48012200-48018200	Weak transcription	Spleen	Spleen
20	chr2:48012200-48019800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:48012200-48021200	Weak transcription	HMEC	breast
22	chr2:48012200-48021600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:48012200-48021600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:48012200-48022000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:48012200-48022200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:48012200-48022200	Weak transcription	Osteobl	bone
27	chr2:48012200-48023000	Weak transcription	NHLF	lung
28	chr2:48012200-48023600	Weak transcription	Left Ventricle	heart
29	chr2:48012200-48024600	Weak transcription	Right Ventricle	heart
30	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
31	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:48012400-48016800	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:48012400-48018000	Weak transcription	Brain Germinal Matrix	brain
34	chr2:48012400-48018200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:48012400-48019400	Weak transcription	NH-A	brain
36	chr2:48012600-48017200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:48012600-48023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:48012600-48023800	Weak transcription	Colonic Mucosa	Colon
39	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr2:48012800-48016800	Weak transcription	Fetal Intestine Small	intestine
41	chr2:48013200-48018200	Weak transcription	Adipose Nuclei	Adipose
42	chr2:48013200-48021600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:48013400-48016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:48013400-48016400	Weak transcription	A549	lung
45	chr2:48013400-48017000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:48013400-48017000	Weak transcription	Fetal Intestine Large	intestine
47	chr2:48013400-48017200	Weak transcription	Pancreas	Pancrea
48	chr2:48013400-48017200	Weak transcription	HSMM	muscle
49	chr2:48013400-48017400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:48013400-48018200	Weak transcription	Fetal Brain Female	brain

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