Variant report

Variant	rs1052447
Chromosome Location	chr1:179711649-179711650
allele	G/T
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	E2F6	chr1:179711602-179713485	H1-hESC	embryonic stem cell:	n/a	chr1:179712478-179712488 chr1:179712734-179712743 chr1:179713026-179713035
2	MAX	chr1:179711632-179713229	H1-hESC	embryonic stem cell:	n/a	chr1:179713027-179713037 chr1:179713049-179713059
3	SUZ12	chr1:179711443-179714153	NT2-D1	testis:	n/a	n/a
4	SIN3A	chr1:179711528-179712544	H1-hESC	embryonic stem cell:	n/a	chr1:179712163-179712177
5	MXI1	chr1:179710798-179717112	SK-N-SH	brain:	n/a	n/a
6	SUZ12	chr1:179711517-179714476	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM163A-1	chr1:179711490-179711832	ENSG00000243062.1
2	lnc-FAM163A-1	chr1:179711490-179711832	ENSG00000243062.1
3	lnc-FAM163A-1	chr1:179711490-179711844	NONHSAT008204

Variant related genes	Relation type
FAM163A	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10798718	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798720	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798721	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913868	0.90[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913870	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913871	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913872	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10913874	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10913875	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10913876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913877	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913878	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913879	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11588754	0.80[ASN][1000 genomes]
rs12037882	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12047821	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403719	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12403967	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12408874	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562455	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12565113	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12737143	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1391434	0.87[CEU][hapmap]
rs16854559	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs16854629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2245195	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2245610	0.85[ASN][1000 genomes]
rs2245702	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2318386	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2318389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454193	0.89[ASN][1000 genomes]
rs2454195	1.00[ASN][1000 genomes]
rs2454196	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2454197	0.87[ASN][1000 genomes]
rs2487739	0.97[ASN][1000 genomes]
rs2487740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2504032	0.82[ASN][1000 genomes]
rs2504033	0.82[ASN][1000 genomes]
rs2504034	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs2504035	0.85[ASN][1000 genomes]
rs2504038	0.85[ASN][1000 genomes]
rs2504039	1.00[ASN][1000 genomes]
rs2504040	1.00[ASN][1000 genomes]
rs2504041	1.00[ASN][1000 genomes]
rs2504042	1.00[ASN][1000 genomes]
rs2504043	0.85[ASN][1000 genomes]
rs2504048	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs2504049	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2504053	0.90[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs3843267	0.90[CEU][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3845381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845382	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845383	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3856045	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3897919	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs3905117	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs3909014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3909015	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4266841	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4269737	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4469684	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565670	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4651050	0.96[ASN][1000 genomes]
rs60556788	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828370	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663482	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7365663	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	nsv548339	chr1:179686244-179722827	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179711400-179711800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
2	chr1:179711400-179711800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:179711400-179711800	Bivalent Enhancer	Fetal Intestine Small	intestine
4	chr1:179711400-179712000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr1:179711400-179714400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:179711600-179711800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr1:179711600-179711800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr1:179711600-179711800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
9	chr1:179711600-179711800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr1:179711600-179711800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr1:179711600-179711800	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
12	chr1:179711600-179711800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:179711600-179711800	Bivalent Enhancer	Colon Smooth Muscle	Colon
14	chr1:179711600-179711800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
15	chr1:179711600-179711800	Bivalent Enhancer	Fetal Intestine Large	intestine
16	chr1:179711600-179712000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
17	chr1:179711600-179712000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
18	chr1:179711600-179712000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:179711600-179712000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:179711600-179712000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:179711600-179712000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:179711600-179712000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr1:179711600-179712000	Bivalent Enhancer	Fetal Stomach	stomach
24	chr1:179711600-179712000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
25	chr1:179711600-179712400	Bivalent Enhancer	Fetal Brain Male	brain
26	chr1:179711600-179712400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
27	chr1:179711600-179712400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
28	chr1:179711600-179712400	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr1:179711600-179713200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
30	chr1:179711600-179713200	Bivalent Enhancer	Fetal Lung	lung
31	chr1:179711600-179713400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:179711600-179713600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:179711600-179713800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr1:179711600-179713800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:179711600-179713800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr1:179711600-179714000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
37	chr1:179711600-179714000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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