Variant report

Variant	rs703667
Chromosome Location	chr12:105067844-105067845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105067366..105069246-chr12:105069344..105071422,3	MCF-7	breast:
2	chr12:104850296..104852857-chr12:105066899..105068579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12579373	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12581376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12581735	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12581769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs56176681	0.91[ASN][1000 genomes]
rs58731514	0.88[ASN][1000 genomes]
rs703664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703666	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs703668	0.89[ASW][hapmap];0.86[CEU][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs703669	0.89[ASW][hapmap];0.86[CEU][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap]
rs703670	0.86[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs703671	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703672	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703673	0.89[ASW][hapmap];0.86[CEU][hapmap];0.86[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs703674	0.84[ASW][hapmap];0.86[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs703675	0.84[ASW][hapmap];0.86[CEU][hapmap];0.91[TSI][hapmap]
rs703676	0.82[AFR][1000 genomes]
rs703677	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703678	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703679	0.86[CEU][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73390104	0.91[ASN][1000 genomes]
rs7954613	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7964130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs835226	0.85[CEU][hapmap]
rs861345	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs703667	SCYL2	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105060200-105068400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:105061000-105068000	Enhancers	Fetal Muscle Leg	muscle
3	chr12:105061000-105068200	Enhancers	Fetal Stomach	stomach
4	chr12:105061200-105068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:105062000-105068000	Enhancers	NHLF	lung
6	chr12:105062000-105068400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:105062800-105068400	Enhancers	Fetal Heart	heart
8	chr12:105063400-105068600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:105063600-105068200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:105063600-105068400	Enhancers	Rectal Smooth Muscle	rectum
11	chr12:105063800-105068400	Enhancers	Colon Smooth Muscle	Colon
12	chr12:105065400-105076000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:105065600-105075400	Weak transcription	Primary T cells from cord blood	blood
14	chr12:105065800-105068000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:105066000-105068000	Weak transcription	Aorta	Aorta
16	chr12:105066000-105068000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:105066000-105068200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:105066000-105071200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:105066000-105072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:105066000-105073000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:105066000-105073600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:105066000-105073800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:105066000-105074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:105066000-105074000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:105066200-105068000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:105066200-105068000	Enhancers	Stomach Smooth Muscle	stomach
27	chr12:105066200-105068000	Enhancers	GM12878-XiMat	blood
28	chr12:105066200-105068200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:105066200-105070600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:105066200-105070600	Weak transcription	Fetal Brain Male	brain
31	chr12:105066200-105071000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:105066200-105073200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:105066200-105073600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:105066200-105074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:105066200-105074200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:105066400-105068000	Enhancers	HSMMtube	muscle
37	chr12:105066400-105068200	Enhancers	NHDF-Ad	bronchial
38	chr12:105066400-105074200	Weak transcription	Thymus	Thymus
39	chr12:105066600-105068200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:105066600-105068400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:105066600-105068800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr12:105066600-105068800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr12:105066600-105069400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:105066600-105069800	Weak transcription	Primary B cells from cord blood	blood
45	chr12:105066600-105070400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:105066600-105070600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:105066600-105070800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:105066600-105070800	Weak transcription	Esophagus	oesophagus
49	chr12:105066600-105073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:105066600-105073400	Weak transcription	Spleen	Spleen

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