Variant report

Variant	rs3748698
Chromosome Location	chr1:214820299-214820300
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	POLR2A	chr1:214812256-214825434	K562	blood:	n/a	n/a
2	POLR2A	chr1:214820197-214820720	K562	blood:	n/a	n/a
3	BACH1	chr1:214819730-214820815	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214819649..214821751-chr1:214822324..214824607,2	K562	blood:
2	chr1:214786498..214788310-chr1:214819229..214821847,2	K562	blood:

Variant related genes	Relation type
CENPF	TF binding region
ENSG00000224584	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10494983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11120355	0.92[MEX][hapmap]
rs11120372	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11801893	0.81[ASN][1000 genomes]
rs11805402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058704	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12067133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12071057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12081395	0.83[AMR][1000 genomes]
rs12096879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12097817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12097854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12404854	0.92[AMR][1000 genomes]
rs12405890	0.97[AMR][1000 genomes]
rs12405995	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12408129	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12408153	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12410075	0.94[AMR][1000 genomes]
rs17023274	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17023275	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17023278	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17023282	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17023284	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17023293	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17023299	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17023338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17023380	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070066	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280049	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2292377	0.97[AMR][1000 genomes]
rs2292378	0.94[AMR][1000 genomes]
rs2292379	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3748692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3748695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790648	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790649	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795514	1.00[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3795516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795518	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795524	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41303281	0.97[AMR][1000 genomes]
rs57338227	0.81[ASN][1000 genomes]
rs58247244	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58724390	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59918378	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60944459	0.92[AMR][1000 genomes]
rs61546198	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6669573	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7533166	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]

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	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997864	chr1:214778658-214994142	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1002937	chr1:214793813-214994142	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1013284	chr1:214799847-214951184	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv873165	chr1:214802299-214889859	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3748698	C1orf227	cis	parietal	SCAN
rs3748698	DTL	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214777600-214838600	Weak transcription	Esophagus	oesophagus
2	chr1:214777800-214838400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:214778000-214839200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:214783400-214838800	Weak transcription	Fetal Kidney	kidney
5	chr1:214784600-214834000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:214785600-214843800	Strong transcription	Fetal Thymus	thymus
7	chr1:214786200-214843000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:214786600-214833800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:214786600-214843200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:214786800-214843800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:214787600-214842200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:214788200-214820600	Weak transcription	Fetal Heart	heart
13	chr1:214789000-214837400	Weak transcription	Small Intestine	intestine
14	chr1:214794400-214833200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:214795200-214838600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:214801000-214839600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:214801000-214843000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:214801200-214846000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:214801800-214841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:214801800-214842600	Strong transcription	A549	lung
21	chr1:214801800-214844800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:214802000-214820400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:214802000-214842000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:214802400-214841600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:214803400-214820400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:214804000-214858200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:214804200-214839400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:214805800-214845800	Strong transcription	Dnd41	blood
29	chr1:214806000-214840200	Weak transcription	Fetal Intestine Small	intestine
30	chr1:214810400-214847400	Weak transcription	Brain Germinal Matrix	brain
31	chr1:214810800-214821600	Strong transcription	HepG2	liver
32	chr1:214811000-214825400	Strong transcription	HSMM	muscle
33	chr1:214811200-214823400	Strong transcription	NHEK	skin
34	chr1:214811200-214841600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:214811400-214841600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:214811600-214825200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:214811600-214833600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:214811600-214840400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:214811800-214823400	Strong transcription	HMEC	breast
40	chr1:214811800-214833800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:214812000-214820600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:214812000-214825400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:214812000-214840600	Strong transcription	Thymus	Thymus
44	chr1:214812200-214834200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:214812600-214829200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:214812800-214822000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:214812800-214846000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:214813400-214840600	Strong transcription	HUVEC	blood vessel
49	chr1:214814200-214841400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:214814400-214823600	Strong transcription	NHDF-Ad	bronchial

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