Variant report

Variant	rs3136247
Chromosome Location	chr2:48013099-48013100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
2	chr2:48013018..48016361-chr2:48016765..48019577,4	K562	blood:
3	chr2:48011141..48015679-chr2:48023292..48025475,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235369	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1042820	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12620679	0.84[YRI][hapmap]
rs1800932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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]
rs3136249	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136279	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3136283	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3136284	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3136288	0.82[CEU][hapmap];1.00[YRI][hapmap];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3136247	FOXN2	cis	parietal	SCAN
rs3136247	MSH6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48009400-48013400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr2:48009400-48013400	Active TSS	Ovary	ovary
3	chr2:48010000-48013400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:48011400-48015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:48011600-48013400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr2:48011600-48013400	Enhancers	Fetal Brain Male	brain
7	chr2:48011600-48014200	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:48011600-48014200	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr2:48011800-48013400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:48011800-48013400	Enhancers	Pancreas	Pancrea
11	chr2:48011800-48013600	Enhancers	Primary B cells from cord blood	blood
12	chr2:48011800-48014400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:48011800-48023000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:48011800-48026200	Weak transcription	Stomach Mucosa	stomach
15	chr2:48012000-48013400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:48012000-48013400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:48012000-48013400	Enhancers	Colon Smooth Muscle	Colon
18	chr2:48012000-48013400	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:48012000-48013400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:48012000-48013400	Enhancers	Fetal Heart	heart
21	chr2:48012000-48014000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:48012000-48014400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:48012000-48014400	Genic enhancers	Fetal Thymus	thymus
24	chr2:48012000-48015000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr2:48012000-48015200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:48012000-48017600	Weak transcription	Fetal Kidney	kidney
27	chr2:48012000-48018000	Weak transcription	Psoas Muscle	Psoas
28	chr2:48012000-48018400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:48012000-48019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:48012000-48022800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:48012000-48023000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:48012000-48023400	Weak transcription	HSMMtube	muscle
33	chr2:48012000-48024400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr2:48012000-48024600	Weak transcription	Aorta	Aorta
35	chr2:48012000-48024600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:48012000-48024800	Weak transcription	NHEK	skin
37	chr2:48012000-48026000	Weak transcription	Esophagus	oesophagus
38	chr2:48012000-48026000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:48012000-48026200	Weak transcription	Gastric	stomach
40	chr2:48012200-48013200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:48012200-48013400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:48012200-48013400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:48012200-48013400	Enhancers	Stomach Smooth Muscle	stomach
44	chr2:48012200-48013400	Genic enhancers	HepG2	liver
45	chr2:48012200-48013600	Enhancers	Brain Anterior Caudate	brain
46	chr2:48012200-48013600	Genic enhancers	Fetal Stomach	stomach
47	chr2:48012200-48014400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:48012200-48014400	Enhancers	Brain Hippocampus Middle	brain
49	chr2:48012200-48014800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:48012200-48017400	Weak transcription	Muscle Satellite Cultured Cells	--

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