Variant report

Variant	rs1704879
Chromosome Location	chr12:104971574-104971575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104970339..104972432-chr12:104974427..104977071,2	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1622100	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1650126	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1650127	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs1704878	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17207200	0.87[ASW][hapmap]
rs2665741	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313316	0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs313317	0.87[ASW][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs313318	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs313324	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1704879	UTP20	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104950000-104978800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104958400-104972400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104961800-104972800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:104963400-104974800	Weak transcription	Gastric	stomach
5	chr12:104964200-104974800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:104964200-104976000	Weak transcription	Primary T cells from cord blood	blood
7	chr12:104964400-104972800	Weak transcription	Spleen	Spleen
8	chr12:104965200-104975400	Weak transcription	Placenta	Placenta
9	chr12:104965400-104971600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:104965400-104971600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:104965400-104982200	Weak transcription	Left Ventricle	heart
12	chr12:104968800-104974200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:104968800-104977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:104968800-104977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:104969000-104971600	Enhancers	Primary hematopoietic stem cells	blood
16	chr12:104969000-104973400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:104969000-104977400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:104969000-104978000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:104969200-104972600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:104969600-104974800	Weak transcription	Pancreas	Pancrea
21	chr12:104969800-104973800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:104969800-104974600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:104970000-104977200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr12:104970200-104975400	Weak transcription	Thymus	Thymus
25	chr12:104970400-104971800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:104970400-104972000	Enhancers	A549	lung
27	chr12:104970400-104973800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:104970400-104975000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:104970400-104978400	Enhancers	Fetal Thymus	thymus
30	chr12:104970600-104972000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr12:104970600-104972400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:104970600-104973200	Enhancers	NHLF	lung
33	chr12:104970600-104973400	Weak transcription	Primary B cells from cord blood	blood
34	chr12:104970600-104973600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:104970600-104973600	Enhancers	GM12878-XiMat	blood
36	chr12:104970600-104974000	Enhancers	HSMM	muscle
37	chr12:104970600-104974200	Enhancers	NHDF-Ad	bronchial
38	chr12:104970800-104971600	Weak transcription	Dnd41	blood
39	chr12:104970800-104973000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:104971000-104972600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:104971000-104972800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:104971000-104973000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:104971000-104973000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:104971000-104973200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:104971000-104990600	Weak transcription	Lung	lung
46	chr12:104971200-104971600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:104971200-104971800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:104971200-104971800	Transcr. at gene 5' and 3'	K562	blood
49	chr12:104971200-104972000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:104971200-104972200	Enhancers	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links