Variant report

Variant	rs7310869
Chromosome Location	chr12:46665386-46665387
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:46665301-46665425	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:46658963-46665919	GM12891	blood:	n/a	n/a
3	POLR2A	chr12:46664788-46665414	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:46664699-46665461	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:46660034-46665824	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46664868..46666420-chr12:46696622..46698481,2	MCF-7	breast:
2	chr12:46562964..46565138-chr12:46663936..46666612,3	MCF-7	breast:
3	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
4	chr12:46660942..46665525-chr12:46775819..46780739,12	MCF-7	breast:
5	chr12:46382717..46386243-chr12:46660668..46665434,7	MCF-7	breast:
6	chr12:46663312..46666406-chr12:46754623..46758323,3	K562	blood:
7	chr12:46664274..46666406-chr12:46754623..46757460,2	K562	blood:

No data

Variant related genes	Relation type
SLC38A1	TF binding region
ENSG00000257261	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10467213	0.86[EUR][1000 genomes]
rs1060735	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1079780	0.80[EUR][1000 genomes]
rs10880947	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880953	0.87[EUR][1000 genomes]
rs11183420	0.93[EUR][1000 genomes]
rs11183441	0.87[EUR][1000 genomes]
rs11504511	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12298619	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12302984	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12310125	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12311507	0.87[EUR][1000 genomes]
rs12317787	0.81[EUR][1000 genomes]
rs12580583	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12816358	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs12816413	0.87[EUR][1000 genomes]
rs1471223	0.81[EUR][1000 genomes]
rs1492892	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1492894	0.81[EUR][1000 genomes]
rs1586905	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2018424	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2087834	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2169030	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2172398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279560	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2408496	0.82[EUR][1000 genomes]
rs2408504	0.87[EUR][1000 genomes]
rs2408505	0.88[EUR][1000 genomes]
rs2408506	0.84[EUR][1000 genomes]
rs2408508	0.81[EUR][1000 genomes]
rs34119192	0.88[EUR][1000 genomes]
rs35123676	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35497251	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782904	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4238102	0.86[EUR][1000 genomes]
rs4438106	0.88[EUR][1000 genomes]
rs4547171	0.81[EUR][1000 genomes]
rs4586238	0.86[EUR][1000 genomes]
rs4768110	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768111	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768113	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768115	0.81[EUR][1000 genomes]
rs4768116	0.81[EUR][1000 genomes]
rs4768694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768695	0.87[EUR][1000 genomes]
rs4768696	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4768698	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs59919892	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6582625	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7132228	0.81[EUR][1000 genomes]
rs7134855	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7297536	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7314069	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315493	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7316127	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7316773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953659	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7958774	0.86[EUR][1000 genomes]
rs7960147	0.88[CEU][hapmap]
rs7961994	0.88[CEU][hapmap]
rs7965629	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7966288	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7967669	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968173	0.88[CEU][hapmap]
rs7968283	0.88[CEU][hapmap]
rs7970911	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7974529	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7976362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979514	0.87[EUR][1000 genomes]
rs7980775	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs898242	0.87[EUR][1000 genomes]
rs956910	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs9669051	0.80[EUR][1000 genomes]
rs9795971	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46664000-46675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:46664200-46665400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:46664200-46677400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:46664400-46665400	Active TSS	GM12878-XiMat	blood
5	chr12:46664400-46665600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:46664400-46666000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:46664400-46666000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr12:46664400-46666400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:46664400-46666600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:46664400-46673800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:46664600-46665400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:46664600-46665600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:46664600-46666800	Enhancers	Primary T cells from cord blood	blood
14	chr12:46664600-46667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:46664600-46667200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:46664800-46665400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:46664800-46665800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:46664800-46670000	Weak transcription	Primary B cells from cord blood	blood
19	chr12:46664800-46671800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:46665000-46665400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:46665000-46665400	Enhancers	Thymus	Thymus
22	chr12:46665000-46665600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:46665000-46666000	Enhancers	Fetal Thymus	thymus
24	chr12:46665000-46666200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr12:46665000-46667600	Enhancers	Fetal Muscle Leg	muscle
26	chr12:46665200-46665400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:46665200-46665400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:46665200-46665400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr12:46665200-46665600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:46665200-46670600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:46665200-46671600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:46665200-46673200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:46665200-46673400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:46665200-46677200	Weak transcription	H1 Cell Line	embryonic stem cell

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