Variant report

Variant	rs3813605
Chromosome Location	chr1:84970947-84970948
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:137)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:137 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:84970873-84971303	HepG2	liver:	n/a	n/a
2	JUN	chr1:84970079-84973077	K562	blood:	n/a	chr1:84970176-84970185 chr1:84972305-84972317 chr1:84972307-84972316
3	ARID3A	chr1:84970808-84971465	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:84969985-84972746	HCT-116	colon:	n/a	n/a
5	MXI1	chr1:84970410-84973047	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:84970863-84972828	GM18526	blood:	n/a	n/a
7	MYC	chr1:84970758-84971361	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:84970808-84971620	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:84970891-84972710	PFSK-1	brain:	n/a	n/a
10	MAX	chr1:84970764-84972587	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:84970344-84972750	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:84970407-84973119	GM19099	blood:	n/a	n/a
13	POLR2A	chr1:84970141-84972678	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:84970931-84972928	K562	blood:	n/a	n/a
15	TEAD4	chr1:84970725-84971356	HepG2	liver:	n/a	n/a
16	EP300	chr1:84970833-84971399	HepG2	liver:	n/a	chr1:84971155-84971169
17	POLR2A	chr1:84970276-84972805	Hela-S3	cervix:	n/a	n/a
18	PML	chr1:84970167-84973030	GM12878	blood:	n/a	n/a
19	SMC3	chr1:84970269-84972875	Hela-S3	cervix:	n/a	chr1:84972211-84972219
20	POLR2A	chr1:84970756-84971058	MCF-7	breast:	n/a	n/a
21	TBP	chr1:84970234-84971496	Hela-S3	cervix:	n/a	n/a
22	NFATC1	chr1:84970321-84971066	GM12878	blood:	n/a	n/a
23	RCOR1	chr1:84970161-84972710	Hela-S3	cervix:	n/a	n/a
24	MXI1	chr1:84969756-84973236	IMR90	lung:	n/a	n/a
25	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
26	HEY1	chr1:84970857-84972714	K562	blood:	n/a	n/a
27	POLR2A	chr1:84970922-84972590	HepG2	liver:	n/a	n/a
28	RXRA	chr1:84970883-84971232	HepG2	liver:	n/a	chr1:84971028-84971037
29	RELA	chr1:84970322-84972863	GM18505	blood:	n/a	n/a
30	TEAD4	chr1:84970869-84972817	K562	blood:	n/a	n/a
31	RAD21	chr1:84970942-84972637	IMR90	lung:	n/a	n/a
32	EBF1	chr1:84970370-84971572	GM12878	blood:	n/a	chr1:84970547-84970558
33	MYC	chr1:84970825-84972868	K562	blood:	n/a	n/a
34	HDAC2	chr1:84970909-84971218	HepG2	liver:	n/a	n/a
35	GTF2F1	chr1:84970873-84971580	Hela-S3	cervix:	n/a	n/a
36	TBL1XR1	chr1:84970903-84972867	K562	blood:	n/a	n/a
37	NFIC	chr1:84970858-84971258	HepG2	liver:	n/a	n/a
38	MAX	chr1:84970795-84972663	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:84970933-84971160	ECC-1	luminal epithelium:	n/a	n/a
40	MYC	chr1:84970667-84972814	NB4	blood:	n/a	n/a
41	MAX	chr1:84970330-84972931	NB4	blood:	n/a	n/a
42	POLR2A	chr1:84970149-84973052	PBDE	blood:	n/a	n/a
43	RUNX3	chr1:84970121-84971121	GM12878	blood:	n/a	n/a
44	RELA	chr1:84970344-84972776	GM15510	blood:	n/a	n/a
45	POLR2A	chr1:84970263-84972827	MCF10A-Er-Src	breast:	n/a	n/a
46	FOXM1	chr1:84970804-84972061	ECC-1	luminal epithelium:	n/a	n/a
47	FOXA2	chr1:84970877-84971223	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:84970011-84973130	IMR90	lung:	n/a	n/a
49	EP300	chr1:84970897-84972452	HepG2	liver:	n/a	chr1:84971559-84971575 chr1:84971155-84971169
50	MAX	chr1:84970885-84972675	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
3	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
4	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
5	chr1:84969596..84972494-chr1:85154864..85156849,3	K562	blood:
6	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
7	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
8	chr1:84970551..84971520-chr5:151151462..151152365,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SPATA1	TF binding region
GNG5	TF binding region
ENSG00000271576	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000177556	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000145907	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11163971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163980	0.81[CHB][hapmap]
rs11163981	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11163992	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144276	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11578494	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11586006	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071149	0.81[CHB][hapmap]
rs12123381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124568	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126584	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]
rs12126924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12128801	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs12136756	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137559	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143652	0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12145405	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1246159	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1395416	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395417	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17109982	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110030	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17110519	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];0.89[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1911159	0.81[CHB][hapmap]
rs2271620	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];0.84[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292191	0.82[CHD][hapmap]
rs2292808	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659173	0.81[CHB][hapmap]
rs2794218	0.81[CHB][hapmap]
rs312395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs312397	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs3813607	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922538	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906995	0.81[CHB][hapmap]
rs4907076	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[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];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907078	0.81[CHB][hapmap]
rs56212819	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57245302	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57442052	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704211	0.81[CHB][hapmap]
rs74095416	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74095424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095432	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095436	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513490	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514763	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];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535445	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7536988	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925740	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3813605	SPATA1	cis	parietal	SCAN
rs3813605	ZSWIM1	trans	cerebellum	SCAN
rs3813605	SPATA1	cis	multi-tissue	Pritchard
rs3813605	CTBS	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:84968600-84971400	Active TSS	Right Atrium	heart
3	chr1:84968800-84973200	Active TSS	Right Ventricle	heart
4	chr1:84969000-84973000	Active TSS	Left Ventricle	heart
5	chr1:84969200-84973200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:84969400-84971200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:84969400-84971400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:84969400-84973200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:84969600-84971200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:84969800-84971000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr1:84969800-84971000	Flanking Active TSS	Dnd41	blood
12	chr1:84969800-84973000	Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:84969800-84973000	Active TSS	Aorta	Aorta
14	chr1:84969800-84973000	Active TSS	HSMM	muscle
15	chr1:84970000-84971000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:84970000-84971000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:84970000-84971000	Flanking Active TSS	Fetal Brain Female	brain
18	chr1:84970000-84971200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr1:84970000-84971200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:84970000-84972800	Active TSS	Ovary	ovary
21	chr1:84970000-84973000	Active TSS	Stomach Smooth Muscle	stomach
22	chr1:84970000-84973200	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:84970000-84973200	Active TSS	Fetal Intestine Large	intestine
24	chr1:84970000-84973600	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr1:84970000-84973600	Active TSS	GM12878-XiMat	blood
26	chr1:84970000-84973600	Active TSS	NHLF	lung
27	chr1:84970200-84971000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr1:84970200-84971000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr1:84970200-84971200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr1:84970200-84971200	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr1:84970200-84971200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr1:84970200-84972800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:84970200-84972800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:84970200-84973000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:84970200-84973000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:84970200-84973000	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:84970200-84973000	Active TSS	HSMMtube	muscle
40	chr1:84970200-84973000	Active TSS	NH-A	brain
41	chr1:84970200-84973200	Active TSS	Psoas Muscle	Psoas
42	chr1:84970200-84973200	Active TSS	NHDF-Ad	bronchial
43	chr1:84970200-84973400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:84970200-84973400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:84970400-84971000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:84970400-84971000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr1:84970400-84971200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:84970400-84971200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr1:84970400-84971200	Active TSS	HepG2	liver
50	chr1:84970400-84971400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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