Variant report

Variant	rs3136315
Chromosome Location	chr2:48022760-48022761
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48018260..48021014-chr2:48021762..48023287,2	K562	blood:
2	chr2:48016148..48017945-chr2:48020322..48022937,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO11-6	chr2:48022339-48023461	NONHSAT070598

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1042820	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1800932	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136235	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3136240	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136241	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136247	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136249	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136269	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136279	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136283	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136284	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3136288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927047	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57632619	0.83[AFR][1000 genomes]
rs58419715	0.83[AFR][1000 genomes]
rs60444285	0.83[AFR][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	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
2	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
3	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
rs3136315	MSH6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48011800-48023000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
6	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
8	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:48012000-48024800	Weak transcription	NHEK	skin
10	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
11	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:48012000-48026200	Weak transcription	Gastric	stomach
13	chr2:48012200-48023000	Weak transcription	NHLF	lung
14	chr2:48012200-48023600	Weak transcription	Left Ventricle	heart
15	chr2:48012200-48024600	Weak transcription	Right Ventricle	heart
16	chr2:48012200-48026000	Weak transcription	Small Intestine	intestine
17	chr2:48012200-48030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:48012600-48023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:48012600-48023800	Weak transcription	Colonic Mucosa	Colon
20	chr2:48012600-48065000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:48013400-48022800	Weak transcription	HUVEC	blood vessel
22	chr2:48013400-48023000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:48013400-48023400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:48013400-48023600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:48013400-48023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:48013400-48023800	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:48013400-48023800	Weak transcription	Fetal Brain Male	brain
28	chr2:48013400-48024200	Weak transcription	Fetal Heart	heart
29	chr2:48013400-48025800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:48014000-48023000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:48014200-48023000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:48015000-48029600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:48016000-48029600	Strong transcription	Fetal Thymus	thymus
34	chr2:48016200-48029600	Strong transcription	Fetal Stomach	stomach
35	chr2:48016200-48030000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:48016200-48050400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:48016400-48029800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:48016600-48025800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:48016600-48030000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:48016800-48030200	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:48017000-48036200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr2:48017000-48049400	Strong transcription	Fetal Intestine Large	intestine
43	chr2:48017200-48024800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:48017200-48025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:48017200-48053200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:48017400-48032200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:48017400-48049600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:48017800-48037800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:48018000-48025800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:48018000-48030200	Strong transcription	Brain Germinal Matrix	brain

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