Variant report

Variant	rs10863819
Chromosome Location	chr1:210502580-210502581
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	EBF1	chr1:210502303-210502606	GM12878	blood:	n/a	n/a
2	ELF1	chr1:210502202-210503020	MCF-7	breast:	n/a	chr1:210502627-210502639 chr1:210502424-210502433
3	ELK1	chr1:210502285-210502925	GM12878	blood:	n/a	n/a
4	EGR1	chr1:210502511-210502845	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:210502534-210502791	HepG2	liver:	n/a	n/a
6	TAF1	chr1:210501934-210502855	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:210501985-210503130	GM12878	blood:	n/a	n/a
8	ATF2	chr1:210502340-210502713	GM12878	blood:	n/a	n/a
9	MTA3	chr1:210502243-210502974	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:210501914-210502856	ProgFib	skin:	n/a	n/a
11	EBF1	chr1:210502449-210502769	GM12878	blood:	n/a	n/a
12	RELA	chr1:210502182-210503113	GM19099	blood:	n/a	n/a
13	POLR2A	chr1:210501883-210503031	GM12878	blood:	n/a	n/a
14	EP300	chr1:210502121-210502591	HepG2	liver:	n/a	chr1:210502345-210502354 chr1:210502165-210502181
15	ELF1	chr1:210502393-210503029	MCF-7	breast:	n/a	chr1:210502627-210502639 chr1:210502424-210502433
16	CHD2	chr1:210502291-210502952	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUND	chr1:210502487-210502995	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:210502502-210502894	HL-60	blood:	n/a	n/a
19	POLR2A	chr1:210501989-210502676	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr1:210502010-210502838	A549	lung:	n/a	n/a
21	ELF1	chr1:210502242-210502931	HepG2	liver:	n/a	chr1:210502627-210502639 chr1:210502424-210502433
22	POLR2A	chr1:210501985-210502857	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:210501956-210502958	HCT-116	colon:	n/a	n/a
24	POLR2A	chr1:210501928-210502906	A549	lung:	n/a	n/a
25	GABPA	chr1:210502186-210502927	MCF-7	breast:	n/a	chr1:210502634-210502643
26	STAT3	chr1:210502516-210503034	MCF10A-Er-Src	breast:	n/a	chr1:210502834-210502841 chr1:210502541-210502552
27	POLR2A	chr1:210501859-210503137	GM12891	blood:	n/a	n/a
28	NFIC	chr1:210502291-210502655	HepG2	liver:	n/a	n/a
29	MAX	chr1:210501714-210503137	A549	lung:	n/a	n/a
30	POLR2A	chr1:210501934-210503014	MCF-7	breast:	n/a	n/a
31	E2F4	chr1:210501813-210503029	MCF10A-Er-Src	breast:	n/a	chr1:210502342-210502352 chr1:210502579-210502591 chr1:210502163-210502172
32	POLR2A	chr1:210501914-210503003	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:210501966-210503031	HUVEC	blood vessel:	n/a	n/a
34	CHD2	chr1:210502475-210502716	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:210501905-210503020	SK-N-SH	brain:	n/a	n/a
36	MAX	chr1:210501848-210503014	A549	lung:	n/a	n/a
37	STAT3	chr1:210502326-210503085	MCF10A-Er-Src	breast:	n/a	chr1:210502834-210502841 chr1:210502541-210502552
38	POLR2A	chr1:210502519-210502895	GM12891	blood:	n/a	n/a
39	RELA	chr1:210501928-210503105	GM18951	blood:	n/a	n/a
40	MAX	chr1:210502342-210502869	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr1:210501858-210502860	A549	lung:	n/a	n/a
42	POLR2A	chr1:210501769-210503128	GM12878	blood:	n/a	n/a
43	TCF12	chr1:210501839-210503028	A549	lung:	n/a	n/a
44	CREB1	chr1:210501940-210502691	GM12878	blood:	n/a	n/a
45	SIN3AK20	chr1:210502146-210502698	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr1:210501979-210502985	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr1:210501846-210503033	GM12892	blood:	n/a	n/a
48	POLR2A	chr1:210502563-210502787	ECC-1	luminal epithelium:	n/a	n/a
49	EP300	chr1:210502330-210503063	GM12878	blood:	n/a	chr1:210502345-210502354 chr1:210502627-210502636
50	POLR2A	chr1:210502021-210502915	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:210499300..210503346-chr1:210545682..210548805,5	K562	blood:
2	chr1:210497683..210507034-chr1:210544536..210549319,22	MCF-7	breast:
3	chr1:210405800..210407964-chr1:210502205..210503882,2	MCF-7	breast:
4	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:

Variant related genes	Relation type
HHAT	TF binding region
ENSG00000203706	Chromatin interaction
ENSG00000082497	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1005174	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10489383	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10489385	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs10489386	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10863820	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863822	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10863825	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs11119458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11119462	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119473	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11119475	1.00[ASW][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11119485	1.00[AFR][1000 genomes]
rs12024862	1.00[AFR][1000 genomes]
rs12030512	0.86[AFR][1000 genomes]
rs12030856	0.86[AFR][1000 genomes]
rs12034871	0.86[AFR][1000 genomes]
rs12040684	0.86[AFR][1000 genomes]
rs12046133	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs12049137	1.00[AFR][1000 genomes]
rs12062126	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12087955	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12120970	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12134251	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12138216	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs12141780	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12143463	1.00[AFR][1000 genomes]
rs1338288	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1338289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17016002	0.87[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2143591	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294843	1.00[AFR][1000 genomes]
rs2294851	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs2357435	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753230	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs3765865	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs3765866	1.00[AFR][1000 genomes]
rs3765877	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3765878	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3765886	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3819985	1.00[MKK][hapmap]
rs4844520	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844996	0.86[AFR][1000 genomes]
rs4844997	1.00[ASW][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58469250	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58960429	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60154123	0.86[AFR][1000 genomes]
rs628908	1.00[MKK][hapmap]
rs650728	1.00[MKK][hapmap]
rs701943	1.00[MKK][hapmap]
rs701944	1.00[MKK][hapmap]
rs7525927	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10863819	ELK4	cis	cerebellum	SCAN
rs10863819	SYT14	cis	parietal	SCAN
rs10863819	DYRK3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210501400-210502800	Active TSS	Primary T helper naive cells from peripheral blood	blood
2	chr1:210501600-210502800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:210501600-210502800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:210501600-210502800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:210501600-210502800	Active TSS	HSMMtube	muscle
6	chr1:210501600-210503000	Active TSS	A549	lung
7	chr1:210501600-210503200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:210501600-210503200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:210501600-210503200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:210501600-210503200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:210501600-210503200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:210501600-210503200	Active TSS	Fetal Brain Female	brain
13	chr1:210501600-210503400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:210501800-210502600	Active TSS	Spleen	Spleen
15	chr1:210501800-210502800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:210501800-210502800	Active TSS	NH-A	brain
17	chr1:210501800-210502800	Active TSS	Osteobl	bone
18	chr1:210501800-210503000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:210501800-210503000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr1:210501800-210503000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:210501800-210503000	Active TSS	Aorta	Aorta
22	chr1:210501800-210503000	Active TSS	Brain Substantia Nigra	brain
23	chr1:210501800-210503000	Active TSS	Placenta	Placenta
24	chr1:210501800-210503000	Active TSS	Gastric	stomach
25	chr1:210501800-210503000	Active TSS	Ovary	ovary
26	chr1:210501800-210503000	Active TSS	Placenta Amnion	Placenta Amnion
27	chr1:210501800-210503000	Active TSS	Psoas Muscle	Psoas
28	chr1:210501800-210503000	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr1:210501800-210503000	Active TSS	Small Intestine	intestine
30	chr1:210501800-210503200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr1:210501800-210503200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:210501800-210503200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:210501800-210503200	Active TSS	Fetal Intestine Large	intestine
34	chr1:210501800-210503200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:210501800-210503200	Active TSS	Left Ventricle	heart
36	chr1:210501800-210503200	Active TSS	Lung	lung
37	chr1:210501800-210503200	Active TSS	Thymus	Thymus
38	chr1:210501800-210503400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:210501800-210503400	Active TSS	Fetal Kidney	kidney
40	chr1:210502000-210502600	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:210502000-210502600	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:210502000-210502800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:210502000-210502800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:210502000-210502800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
45	chr1:210502000-210502800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
46	chr1:210502000-210502800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:210502000-210502800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:210502000-210502800	Active TSS	Primary monocytes fromperipheralblood	blood
49	chr1:210502000-210502800	Active TSS	Primary B cells from peripheral blood	blood
50	chr1:210502000-210502800	Active TSS	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links