Variant report

Variant	rs10828870
Chromosome Location	chr10:18826813-18826814
allele	C/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	POLR2A	chr10:18826768-18826887	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:18824996..18829139-chr10:18831210..18835804,4	K562	blood:

Variant related genes	Relation type
ENSG00000225527	TF binding region
ENSG00000240291	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10400076	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1055116	0.85[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes]
rs10734063	0.87[AMR][1000 genomes]
rs10741091	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10741101	0.93[ASN][1000 genomes]
rs10741111	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10741115	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs10741127	0.84[CEU][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs10741129	0.82[AMR][1000 genomes]
rs10741132	0.83[AMR][1000 genomes]
rs10764578	0.82[ASN][1000 genomes]
rs10764582	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10764583	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10764600	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10764601	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10764603	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10764625	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10764640	0.84[AMR][1000 genomes]
rs10764691	0.82[AMR][1000 genomes]
rs10828851	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10828871	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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10828872	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10828896	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10828911	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10828965	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10828975	0.85[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10829022	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10829037	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs10829039	0.89[AMR][1000 genomes]
rs10829040	0.81[AMR][1000 genomes]
rs10829058	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes]
rs10829060	0.87[AMR][1000 genomes]
rs10829070	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs10829151	0.92[CEU][hapmap];0.94[CHB][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs10829213	0.82[AMR][1000 genomes]
rs11014634	0.85[ASN][1000 genomes]
rs11014892	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11014981	0.89[JPT][hapmap]
rs11015048	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015196	0.89[AMR][1000 genomes]
rs11015255	0.82[AMR][1000 genomes]
rs11015312	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs11015421	0.87[AMR][1000 genomes]
rs11511084	0.90[JPT][hapmap]
rs11525266	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11540309	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs11815228	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12219183	0.84[AMR][1000 genomes]
rs12359758	0.87[AMR][1000 genomes]
rs12569474	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12762481	0.90[JPT][hapmap]
rs12766105	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs12766314	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12767923	0.90[JPT][hapmap]
rs12769425	0.90[JPT][hapmap]
rs12770851	0.84[JPT][hapmap]
rs12772522	0.89[JPT][hapmap]
rs12778035	0.90[JPT][hapmap]
rs12781208	0.89[JPT][hapmap]
rs12784986	0.90[JPT][hapmap]
rs12785031	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs2228645	0.84[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2272274	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];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740102	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs3740104	0.90[JPT][hapmap]
rs3817494	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4237349	0.90[JPT][hapmap]
rs4310518	0.89[JPT][hapmap]
rs4314963	0.90[JPT][hapmap]
rs4445544	0.89[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs4468242	0.90[JPT][hapmap]
rs4747349	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4747350	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748481	0.88[JPT][hapmap]
rs4748483	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs4748488	0.85[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4748492	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4748496	0.90[JPT][hapmap]
rs4748499	0.90[JPT][hapmap]
rs4748509	0.81[AMR][1000 genomes]
rs5022622	0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs56410858	0.82[AMR][1000 genomes]
rs57066269	0.86[AMR][1000 genomes]
rs57579336	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62634837	0.86[AMR][1000 genomes]
rs62634838	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62636218	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482515	0.87[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6482533	0.85[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6482597	0.85[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes]
rs7072624	0.90[JPT][hapmap]
rs7072963	0.90[JPT][hapmap]
rs7077722	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7079325	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7081461	0.89[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7081690	0.84[AMR][1000 genomes]
rs7081977	0.87[AMR][1000 genomes]
rs7087030	0.83[AMR][1000 genomes]
rs7088091	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7096923	0.90[JPT][hapmap]
rs7099260	0.85[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs7099423	0.90[JPT][hapmap]
rs7100880	0.94[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap]
rs72787951	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72787963	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7894016	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7895784	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap]
rs7897159	0.80[JPT][hapmap]
rs7898513	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7898781	0.87[AMR][1000 genomes]
rs7899017	0.87[AMR][1000 genomes]
rs7901598	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7904016	0.89[JPT][hapmap]
rs7904263	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7904949	0.89[JPT][hapmap]
rs7905365	0.89[JPT][hapmap]
rs7909570	0.82[AMR][1000 genomes]
rs7909845	0.83[AMR][1000 genomes]
rs7917584	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7922550	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7922829	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7923480	0.88[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1042073	chr10:18806900-18838303	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv34545	chr10:18821185-18908294	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10828870	ARL5B	Cis_1M	lymphoblastoid	RTeQTL
rs10828870	NSUN6	cis	lung	GTEx
rs10828870	RP11-499P20.2	cis	lung	GTEx
rs10828870	RP11-499P20.2	cis	Whole Blood	GTEx
rs10828870	NSUN6	Cis_1M	lymphoblastoid	RTeQTL
rs10828870	RP11-499P20.2	cis	Thyroid	GTEx
rs10828870	RP11-499P20.2	cis	Esophagus Mucosa	GTEx
rs10828870	CACNB2	Cis_1M	lymphoblastoid	RTeQTL
rs10828870	ARL5B	cis	multi-tissue	Pritchard
rs10828870	ARL5B	cis	lymphoblastoid	seeQTL
rs10828870	RP11-499P20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10828870	RP11-499P20.2	cis	Nerve Tibial	GTEx
rs10828870	NSUN6	cis	cerebellum	SCAN
rs10828870	NSUN6	cis	parietal	SCAN
rs10828870	TRDMT1	cis	parietal	SCAN
rs10828870	ARL5B	cis	Whole Blood	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18800400-18827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr10:18802600-18828000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:18802600-18828200	Weak transcription	Lung	lung
4	chr10:18807400-18828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:18808000-18828000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:18808400-18827000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:18809000-18827000	Weak transcription	Small Intestine	intestine
8	chr10:18810400-18828000	Weak transcription	Brain Angular Gyrus	brain
9	chr10:18810600-18827000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:18810600-18828200	Weak transcription	Aorta	Aorta
11	chr10:18810800-18828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr10:18812400-18827000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr10:18812800-18827000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:18814000-18828000	Weak transcription	Esophagus	oesophagus
15	chr10:18814600-18827000	Weak transcription	Thymus	Thymus
16	chr10:18814800-18827600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr10:18815200-18843600	Weak transcription	A549	lung
18	chr10:18815800-18828000	Weak transcription	K562	blood
19	chr10:18816400-18830400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:18816400-18841800	Strong transcription	Liver	Liver
21	chr10:18816800-18829600	Weak transcription	HSMMtube	muscle
22	chr10:18817400-18829000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr10:18818800-18828000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:18818800-18828400	Weak transcription	Fetal Thymus	thymus
25	chr10:18819200-18827000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr10:18819400-18827000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr10:18819600-18827400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr10:18819600-18828000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:18819800-18827400	Weak transcription	Fetal Brain Male	brain
30	chr10:18819800-18829800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:18820000-18828400	Weak transcription	Fetal Muscle Leg	muscle
32	chr10:18820000-18829800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:18820800-18841600	Weak transcription	Hela-S3	cervix
34	chr10:18821000-18827000	Weak transcription	Primary B cells from cord blood	blood
35	chr10:18822000-18827200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr10:18822000-18840400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:18822000-18848000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr10:18822200-18830400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr10:18822400-18829600	Weak transcription	HSMM	muscle
40	chr10:18822400-18833600	Strong transcription	Primary T cells from cord blood	blood
41	chr10:18822600-18829000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:18822600-18830600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:18822800-18830600	Strong transcription	Left Ventricle	heart
44	chr10:18822800-18841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:18823200-18831200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr10:18823400-18830400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr10:18823400-18830600	Strong transcription	Fetal Lung	lung
48	chr10:18823400-18834800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:18823600-18831000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr10:18823600-18836600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links