Variant report

Variant	rs889970
Chromosome Location	chr12:121856217-121856218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121855348-121856392	K562	blood:	n/a	n/a
2	POLR2A	chr12:121856197-121857388	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr12:121855765-121856410	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121733525..121736367-chr12:121853809..121856365,2	K562	blood:
2	chr12:121836753..121839584-chr12:121854108..121857673,4	MCF-7	breast:
3	chr12:121851621..121853222-chr12:121854783..121857476,2	K562	blood:
4	chr12:121851621..121854706-chr12:121854783..121857476,4	K562	blood:
5	chr12:121844680..121849870-chr12:121853843..121857044,5	K562	blood:
6	chr12:121854617..121857156-chr12:121863285..121864940,2	MCF-7	breast:
7	chr12:121835704..121841982-chr12:121855433..121861253,10	K562	blood:
8	chr12:121836245..121838379-chr12:121854480..121857016,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF34	TF binding region
ENSG00000170633	Chromatin interaction
ENSG00000110931	Chromatin interaction
ENSG00000089053	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10444490	0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10744761	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10744762	0.94[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10774592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774593	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849872	0.83[EUR][1000 genomes]
rs10849874	0.86[EUR][1000 genomes]
rs10849876	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849883	0.87[EUR][1000 genomes]
rs10849886	0.96[CEU][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10849888	0.81[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs10849890	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11065566	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065569	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12579582	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1706459	0.83[EUR][1000 genomes]
rs61955091	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6489811	0.94[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7134248	0.87[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7296507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960545	0.83[EUR][1000 genomes]
rs7961855	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7962143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976840	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977709	0.87[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs7980819	0.94[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs889970	TAOK3	cis	parietal	SCAN
rs889970	B3GNT4	cis	cerebellum	SCAN
rs889970	CLIP1	cis	parietal	SCAN
rs889970	TMEM120B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121839000-121861000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:121839000-121866400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:121839000-121866400	Weak transcription	Small Intestine	intestine
4	chr12:121839200-121856800	Weak transcription	HSMMtube	muscle
5	chr12:121839200-121860800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:121841400-121874600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:121850000-121871800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:121850400-121887400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:121850800-121874600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:121851000-121870800	Strong transcription	Fetal Thymus	thymus
11	chr12:121851600-121862200	Strong transcription	GM12878-XiMat	blood
12	chr12:121851600-121862400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:121851600-121872200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:121851600-121874400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:121851800-121861400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:121851800-121861400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:121851800-121869000	Strong transcription	Hela-S3	cervix
18	chr12:121851800-121874600	Strong transcription	Dnd41	blood
19	chr12:121851800-121891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:121852000-121862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:121852000-121862400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:121852000-121862400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:121852000-121874400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:121852200-121858200	Strong transcription	Primary B cells from cord blood	blood
25	chr12:121852200-121861000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:121852200-121862600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:121852200-121863000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:121852200-121871600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:121852200-121872200	Strong transcription	Liver	Liver
30	chr12:121852200-121873400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:121852200-121874400	Strong transcription	Fetal Stomach	stomach
32	chr12:121852200-121883200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:121852200-121884800	Strong transcription	Primary T cells from cord blood	blood
34	chr12:121852400-121857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:121852400-121862600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:121852400-121872000	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:121852400-121874400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:121852400-121881800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:121852600-121861000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:121852600-121861200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:121852600-121872200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:121852600-121881600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr12:121852800-121862200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:121852800-121872000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:121852800-121874200	Strong transcription	Thymus	Thymus
46	chr12:121853000-121874400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:121853000-121884800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr12:121853200-121858600	Strong transcription	HepG2	liver
49	chr12:121853400-121869600	Strong transcription	Osteobl	bone
50	chr12:121853600-121856600	Genic enhancers	Adipose Nuclei	Adipose

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