Variant report

Variant	rs12127697
Chromosome Location	chr1:184505131-184505132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:184504844-184505365	SK-N-SH	brain:	n/a	chr1:184505107-184505128 chr1:184505114-184505123
2	GATA3	chr1:184504500-184505481	SK-N-SH	brain:	n/a	chr1:184505107-184505128 chr1:184505114-184505123

No.	Distal block	Cell Line	Cell type
1	chr1:184493911..184496906-chr1:184501930..184505851,3	K562	blood:
2	chr1:184496059..184498642-chr1:184502199..184505203,5	MCF-7	breast:
3	chr1:184498410..184500025-chr1:184504648..184506680,2	MCF-7	breast:

Variant related genes	Relation type
C1orf21	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10399817	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs10489729	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs10911610	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs11810399	0.80[CEU][hapmap]
rs12117823	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12120604	0.94[CHB][hapmap];0.88[GIH][hapmap];0.85[ASN][1000 genomes]
rs12121612	0.94[CHB][hapmap]
rs12129904	0.93[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs12138103	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12141469	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143271	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1535132	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs16823195	0.94[CHB][hapmap];0.88[GIH][hapmap];0.93[MKK][hapmap];0.83[ASN][1000 genomes]
rs16823197	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16823238	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs16823311	0.81[ASN][1000 genomes]
rs16823313	0.85[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs16823318	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs1969683	0.81[ASN][1000 genomes]
rs2180072	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207526	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs2207527	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35682339	0.95[ASN][1000 genomes]
rs58231072	0.83[ASN][1000 genomes]
rs61643431	0.82[ASN][1000 genomes]
rs61825202	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61825204	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61825205	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659261	0.94[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6669940	0.81[ASN][1000 genomes]
rs6683932	0.94[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6693408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7513091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525267	0.85[ASN][1000 genomes]
rs7530615	0.81[ASN][1000 genomes]
rs7548188	0.85[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12127697	MR1	cis	cerebellum	SCAN
rs12127697	TDRD5	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184474400-184505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:184478400-184505200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:184480200-184505200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:184486800-184505400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:184489800-184505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:184501000-184505200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:184501400-184505400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr1:184501800-184510200	Weak transcription	NHEK	skin
9	chr1:184502400-184505400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:184502400-184517000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:184502400-184520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:184502600-184505200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr1:184502600-184527200	Weak transcription	Fetal Brain Female	brain
14	chr1:184503000-184505200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:184503000-184505400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:184503000-184505400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:184503200-184505400	Weak transcription	Left Ventricle	heart
18	chr1:184503200-184505400	Weak transcription	Lung	lung
19	chr1:184503200-184514600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:184503200-184516400	Weak transcription	Fetal Brain Male	brain
21	chr1:184503400-184515800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:184503400-184520400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:184503800-184505200	Enhancers	Adipose Nuclei	Adipose
24	chr1:184503800-184505200	Enhancers	Fetal Lung	lung
25	chr1:184503800-184505400	Enhancers	HSMM	muscle
26	chr1:184503800-184505400	Enhancers	HSMMtube	muscle
27	chr1:184503800-184505800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:184503800-184506000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr1:184504000-184505200	Strong transcription	Primary hematopoietic stem cells	blood
30	chr1:184504000-184505400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:184504000-184505400	Weak transcription	Pancreas	Pancrea
32	chr1:184504000-184506200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:184504000-184507000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:184504000-184507200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:184504200-184505200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:184504200-184505400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:184504200-184505400	Weak transcription	Brain Anterior Caudate	brain
38	chr1:184504200-184508600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:184504200-184522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:184504400-184505400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:184504400-184505400	Weak transcription	Right Atrium	heart
42	chr1:184504400-184505800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:184504400-184508200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr1:184504400-184508800	Weak transcription	Psoas Muscle	Psoas
45	chr1:184504400-184510600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:184504600-184505400	Weak transcription	Ovary	ovary
47	chr1:184504600-184505800	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:184504800-184505200	Weak transcription	Fetal Stomach	stomach
49	chr1:184504800-184505200	Weak transcription	Right Ventricle	heart
50	chr1:184504800-184505200	Enhancers	NHDF-Ad	bronchial

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