Variant report

Variant	rs7539584
Chromosome Location	chr1:151182953-151182954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151182921-151184181	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151171022..151172547-chr1:151181684..151184627,2	K562	blood:
2	chr1:151181898..151183969-chr1:151189213..151192203,2	MCF-7	breast:
3	chr1:151180789..151184373-chr1:151184663..151188461,3	MCF-7	breast:
4	chr1:151182446..151185055-chr1:151193803..151196662,2	MCF-7	breast:
5	1:151180715-151199990..1:151402394-151411623	GM12878	blood:
6	chr1:151175695..151178568-chr1:151178857..151183674,4	MCF-7	breast:
7	chr1:151171022..151173926-chr1:151179427..151183184,4	K562	blood:
8	chr1:151170441..151172555-chr1:151182780..151185772,2	MCF-7	breast:

No data

Variant related genes	Relation type
PIP5K1A	TF binding region
ENSG00000238711	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10749660	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10888406	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888408	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10888409	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs10888410	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204791	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204795	0.82[ASN][1000 genomes]
rs11807075	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022732	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040384	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048670	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12062719	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080778	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407426	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833079	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]
rs4291501	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4520422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636463	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4970944	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971015	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971016	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4971023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971025	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971026	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs5022636	0.81[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817972	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587562	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681163	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683396	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695344	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6701325	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7521064	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7539584	SELENBP1	cis	cerebellum	SCAN
rs7539584	CTSS	cis	cerebellum	SCAN
rs7539584	ANKRD34A	cis	cerebellum	SCAN
rs7539584	ARNT	cis	parietal	SCAN
rs7539584	PSMD4	cis	cerebellum	SCAN
rs7539584	FLG	cis	cerebellum	SCAN
rs7539584	PSMD4	cis	parietal	SCAN
rs7539584	MRPS21	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151172800-151197200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:151172800-151204400	Weak transcription	Stomach Mucosa	stomach
3	chr1:151173200-151191600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:151173200-151196600	Weak transcription	K562	blood
5	chr1:151173200-151197000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:151173200-151199600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:151173200-151200000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:151173200-151212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:151173600-151210600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:151173800-151185200	Strong transcription	Fetal Intestine Small	intestine
12	chr1:151174000-151194600	Weak transcription	Brain Substantia Nigra	brain
13	chr1:151174000-151199400	Weak transcription	Small Intestine	intestine
14	chr1:151174200-151200600	Weak transcription	Pancreas	Pancrea
15	chr1:151174400-151183600	Strong transcription	Fetal Thymus	thymus
16	chr1:151174400-151183800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:151174400-151187000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:151174400-151189200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:151174400-151203800	Weak transcription	Fetal Brain Male	brain
20	chr1:151174600-151184400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:151174600-151185000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:151174600-151185200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:151174800-151183600	Strong transcription	Primary T cells from cord blood	blood
24	chr1:151175000-151185400	Strong transcription	Fetal Stomach	stomach
25	chr1:151175000-151189000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:151175200-151184000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:151175200-151185200	Weak transcription	Psoas Muscle	Psoas
28	chr1:151175400-151183400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:151175600-151185000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:151175800-151183200	Weak transcription	NH-A	brain
31	chr1:151175800-151193800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:151175800-151199800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:151175800-151200400	Weak transcription	Aorta	Aorta
34	chr1:151176000-151194600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:151176200-151200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:151176600-151196400	Weak transcription	Primary B cells from cord blood	blood
37	chr1:151176600-151197000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:151177200-151183400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:151177400-151185000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:151177600-151183400	Strong transcription	Hela-S3	cervix
41	chr1:151177600-151183600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr1:151177800-151183400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:151178000-151183800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:151178000-151184800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:151178000-151185000	Strong transcription	Fetal Intestine Large	intestine
46	chr1:151178200-151185000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:151178200-151185200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:151178400-151183600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:151178400-151183600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links