Variant report

Variant	rs3176890
Chromosome Location	chr10:97581397-97581398
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	chr10:97580945-97581717	GM12891	blood:	n/a	n/a
2	POLR2A	chr10:97580769-97581865	GM12878	blood:	n/a	n/a
3	NFATC1	chr10:97579122-97581495	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:97580876-97582105	GM12891	blood:	n/a	n/a
5	POLR2A	chr10:97580719-97582128	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:97580730-97581744	GM12891	blood:	n/a	n/a
7	POLR2A	chr10:97580187-97581700	GM12891	blood:	n/a	n/a
8	POLR2A	chr10:97580825-97582126	GM12891	blood:	n/a	n/a
9	POLR2A	chr10:97580958-97581778	GM12892	blood:	n/a	n/a
10	POLR2A	chr10:97581247-97581713	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENTPD1	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10736092	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736093	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10736094	0.98[ASN][1000 genomes]
rs10748642	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10748643	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10748645	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748647	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748649	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10786234	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10786236	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10786237	0.80[ASN][1000 genomes]
rs10882655	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882656	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882657	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10882660	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882663	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882666	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882668	0.87[ASN][1000 genomes]
rs10882669	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10882673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882675	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10882676	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11188445	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188446	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11188449	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11188452	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11188460	0.90[AMR][1000 genomes]
rs11188465	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11188486	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188497	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188513	0.98[ASN][1000 genomes]
rs11517041	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1342790	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342791	0.80[ASN][1000 genomes]
rs1418709	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1539433	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573112	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1891534	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1933165	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1933172	0.86[AMR][1000 genomes]
rs2051052	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2095713	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2153913	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153914	0.98[ASN][1000 genomes]
rs2185818	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2275759	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2861147	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2861148	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2861152	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2901872	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2901873	0.80[ASN][1000 genomes]
rs3176881	0.98[ASN][1000 genomes]
rs3176891	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181124	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3181129	0.83[ASN][1000 genomes]
rs3181131	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181132	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3814159	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3892344	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3929900	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3934409	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4074424	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075310	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322324	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4336961	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4381306	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4396219	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4412693	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4431963	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4539246	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4551688	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4582902	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4614366	0.83[ASN][1000 genomes]
rs4625389	0.93[AMR][1000 genomes]
rs4917705	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4917707	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4917714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4917715	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918960	0.90[AMR][1000 genomes]
rs4918962	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4918968	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4918969	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4918971	0.84[ASN][1000 genomes]
rs4918973	0.80[ASN][1000 genomes]
rs4918974	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5014871	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6584017	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6584018	0.86[AMR][1000 genomes]
rs6584022	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6584023	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6584027	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6584030	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069030	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7071836	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7074403	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7077566	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7082531	0.89[ASN][1000 genomes]
rs7083411	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7083960	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086986	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7088584	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7088961	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7094382	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7094484	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7095587	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7096317	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7097489	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7099844	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7478595	0.86[AMR][1000 genomes]
rs7913082	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7914286	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7921242	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3176890	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs3176890	ENTPD1	cis	multi-tissue	Pritchard
rs3176890	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL
rs3176890	TCTN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97573800-97584400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:97574200-97583000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:97574400-97581400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:97574800-97590800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr10:97575600-97596600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:97575800-97592000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:97575800-97597000	Weak transcription	Brain Hippocampus Middle	brain
8	chr10:97577200-97587200	Weak transcription	Lung	lung
9	chr10:97577200-97591400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr10:97577600-97583000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr10:97578200-97583000	Enhancers	Primary B cells from peripheral blood	blood
12	chr10:97578600-97588800	Weak transcription	Fetal Stomach	stomach
13	chr10:97578600-97604400	Weak transcription	Aorta	Aorta
14	chr10:97579200-97582400	Enhancers	Primary B cells from cord blood	blood
15	chr10:97579400-97581800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr10:97579600-97581400	Enhancers	Fetal Intestine Large	intestine
17	chr10:97580400-97581400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:97580400-97581600	Enhancers	Primary hematopoietic stem cells	blood
19	chr10:97580400-97583200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:97580600-97582600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:97580800-97582000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr10:97581000-97581400	Enhancers	Spleen	Spleen
23	chr10:97581000-97581600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
24	chr10:97581000-97600600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr10:97581200-97581400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr10:97581200-97581800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:97581200-97581800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr10:97581200-97596400	Weak transcription	Small Intestine	intestine
29	chr10:97581200-97602000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links