Variant report

Variant	rs10847227
Chromosome Location	chr12:123066685-123066686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10744287	0.80[YRI][hapmap]
rs10744294	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773378	0.91[ASN][1000 genomes]
rs10847103	0.81[JPT][hapmap]
rs10847235	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11058480	0.81[JPT][hapmap]
rs11058603	0.80[ASN][1000 genomes]
rs11058607	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11058649	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11058721	0.89[ASN][1000 genomes]
rs11058772	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058796	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11058812	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11058868	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058904	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11059008	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11059023	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11059028	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12227778	0.85[JPT][hapmap]
rs12230600	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12819165	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12827322	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12829891	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1392237	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270775	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2277346	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs34031587	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34773022	0.83[EUR][1000 genomes]
rs35139892	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35685258	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35825023	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36008586	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57721222	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61954998	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61956128	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61956132	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6489111	0.98[ASN][1000 genomes]
rs66893471	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7296826	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7297692	0.86[ASN][1000 genomes]
rs7301815	0.92[ASN][1000 genomes]
rs7310366	0.98[ASN][1000 genomes]
rs73409839	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7485035	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7953379	0.88[ASN][1000 genomes]
rs7954964	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7969534	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7976597	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7977922	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979860	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7979863	0.99[ASN][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	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases
3	nsv1054458	chr12:123045662-123133545	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv2761772	chr12:123045674-123115508	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv983478	chr12:123062133-123080307	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10847227	SNRNP35	cis	lymphoblastoid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123012400-123114000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123012400-123117000	Weak transcription	Pancreas	Pancrea
3	chr12:123012400-123121200	Weak transcription	Aorta	Aorta
4	chr12:123012600-123095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:123012800-123097400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:123012800-123109200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:123013000-123076400	Weak transcription	Right Ventricle	heart
8	chr12:123013000-123109200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:123013200-123103000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123013200-123112400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:123013400-123080600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:123013400-123107400	Weak transcription	Fetal Heart	heart
13	chr12:123013400-123120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:123014400-123084000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:123014600-123085400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:123015400-123079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:123015600-123115000	Strong transcription	Dnd41	blood
18	chr12:123022200-123084600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:123022600-123113800	Weak transcription	Colonic Mucosa	Colon
20	chr12:123026000-123076400	Weak transcription	Gastric	stomach
21	chr12:123026000-123081000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:123029200-123085000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:123029200-123107600	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:123032600-123095400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:123033400-123067000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:123036400-123074200	Weak transcription	Fetal Brain Male	brain
27	chr12:123037200-123113000	Weak transcription	Brain Anterior Caudate	brain
28	chr12:123037600-123095400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:123037800-123100600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:123038400-123120000	Weak transcription	Small Intestine	intestine
31	chr12:123042600-123107200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:123042800-123080000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:123043800-123066800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:123043800-123121800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:123046400-123073400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:123046400-123084800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:123047200-123080600	Strong transcription	Fetal Thymus	thymus
38	chr12:123047800-123068600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:123047800-123078800	Strong transcription	Fetal Muscle Leg	muscle
40	chr12:123050600-123073000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:123050800-123112600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:123050800-123115200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:123051000-123072800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr12:123052400-123067600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:123052400-123080200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr12:123052600-123079600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:123053600-123076000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:123053800-123072600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:123055400-123070600	Strong transcription	Fetal Intestine Large	intestine
50	chr12:123056000-123069200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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