Variant report

Variant	rs10863919
Chromosome Location	chr1:211811956-211811957
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	chr1:211811903-211812566	Hela-S3	cervix:	n/a	n/a
2	TFAP2C	chr1:211811691-211813538	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:211811826-211812523	Hela-S3	cervix:	n/a	n/a
4	SMARCC1	chr1:211811409-211812476	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr1:211811877-211813893	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr1:211811911-211812120	NHEK	skin:	n/a	n/a
7	TCF7L2	chr1:211811803-211813778	Hela-S3	cervix:	n/a	chr1:211812465-211812474
8	TBP	chr1:211811945-211812467	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:211811726-211814344	Hela-S3	cervix:	n/a	n/a
10	SMARCC2	chr1:211811895-211812455	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr1:211811829-211812524	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:211811859-211812520	Hela-S3	cervix:	n/a	n/a
13	TFAP2A	chr1:211811767-211813439	Hela-S3	cervix:	n/a	chr1:211812131-211812146
14	MAX	chr1:211811920-211812524	Hela-S3	cervix:	n/a	n/a
15	USF2	chr1:211811857-211812458	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr1:211811915-211813863	Hela-S3	cervix:	n/a	n/a
17	MYC	chr1:211811924-211812550	Hela-S3	cervix:	n/a	n/a
18	MAX	chr1:211811899-211812518	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211747427..211749600-chr1:211810215..211812897,2	K562	blood:
2	chr1:211805954..211807830-chr1:211810555..211812059,2	K562	blood:

Variant related genes	Relation type
ENSG00000227764	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158305	0.85[EUR][1000 genomes]
rs10158307	0.84[EUR][1000 genomes]
rs10158309	0.85[EUR][1000 genomes]
rs10158749	0.86[EUR][1000 genomes]
rs10158790	0.85[EUR][1000 genomes]
rs10158874	0.86[EUR][1000 genomes]
rs10159253	0.85[EUR][1000 genomes]
rs10779564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][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]
rs10779565	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863920	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119780	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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119783	0.80[EUR][1000 genomes]
rs11119786	0.81[EUR][1000 genomes]
rs11119787	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576789	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11577255	0.81[EUR][1000 genomes]
rs12087826	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12090722	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12123429	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142250	0.85[EUR][1000 genomes]
rs12727505	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12741252	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12758005	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs1373293	0.85[EUR][1000 genomes]
rs35531215	0.83[EUR][1000 genomes]
rs4245741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951415	0.91[ASN][1000 genomes]
rs4951416	0.91[CEU][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951418	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951419	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951421	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951537	0.84[ASN][1000 genomes]
rs4951539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951540	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61851777	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540697	0.87[MEX][hapmap]
rs6540698	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660850	0.87[MEX][hapmap]
rs6669878	0.85[EUR][1000 genomes]
rs6670986	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671497	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671506	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675796	0.83[CEU][hapmap]
rs6682640	0.82[AMR][1000 genomes]
rs6693364	0.80[EUR][1000 genomes]
rs7513348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523748	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7527270	1.00[CHB][hapmap]
rs7551699	0.81[EUR][1000 genomes]
rs894853	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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894854	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894855	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10863919	PLXNA2	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:211806800-211813000	Weak transcription	Stomach Mucosa	stomach
4	chr1:211807000-211812000	Weak transcription	Adipose Nuclei	Adipose
5	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
6	chr1:211807000-211816200	Weak transcription	Ovary	ovary
7	chr1:211807200-211812000	Weak transcription	NHLF	lung
8	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
9	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:211807400-211812200	Weak transcription	NH-A	brain
11	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:211807600-211812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:211807600-211812800	Weak transcription	Pancreas	Pancrea
14	chr1:211807600-211813000	Weak transcription	HSMMtube	muscle
15	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
16	chr1:211809400-211813000	Enhancers	A549	lung
17	chr1:211809800-211813000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:211810200-211812000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:211810200-211812000	Weak transcription	HMEC	breast
20	chr1:211810200-211812000	Weak transcription	NHDF-Ad	bronchial
21	chr1:211810200-211812200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:211810200-211813000	Weak transcription	HSMM	muscle
23	chr1:211810400-211812000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:211810600-211812000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:211810600-211816400	Weak transcription	Spleen	Spleen
26	chr1:211810800-211812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:211810800-211812000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:211810800-211812000	Weak transcription	Osteobl	bone
29	chr1:211810800-211812200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:211811000-211812000	Weak transcription	HUVEC	blood vessel
31	chr1:211811200-211813600	Enhancers	Placenta	Placenta
32	chr1:211811400-211812600	Flanking Active TSS	Hela-S3	cervix
33	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
34	chr1:211811600-211812200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:211811600-211812600	Enhancers	Esophagus	oesophagus
36	chr1:211811600-211813000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:211811600-211813000	Enhancers	HepG2	liver
38	chr1:211811600-211815000	Enhancers	Liver	Liver
39	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
40	chr1:211811800-211814000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links