Variant report

Variant	rs1539433
Chromosome Location	chr10:97519645-97519646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97514306..97516090-chr10:97518536..97520817,2	K562	blood:

Variant related genes	Relation type
ENSG00000138185	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10736092	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10736093	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10736094	0.88[ASN][1000 genomes]
rs10748642	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10748645	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10748647	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748648	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10748649	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786234	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10786236	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10882655	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882656	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882657	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882659	0.85[AFR][1000 genomes]
rs10882660	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882663	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10882668	0.80[ASN][1000 genomes]
rs10882669	0.85[EUR][1000 genomes]
rs10882673	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882674	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882675	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882676	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11188445	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188446	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11188449	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188452	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11188460	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188465	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11188486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11188497	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188513	0.88[ASN][1000 genomes]
rs11517041	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1342790	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1418709	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573112	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1891534	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1933165	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1933172	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2051052	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2095713	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2153913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153914	0.88[ASN][1000 genomes]
rs2185818	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2226163	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2275759	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2861147	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2861148	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2861152	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2901872	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3176881	0.88[ASN][1000 genomes]
rs3176890	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3176891	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3181124	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3181131	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3181132	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814159	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3892344	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3929900	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3934409	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4074424	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4075310	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4322324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4336961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4381306	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4396219	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4412693	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4431963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4539246	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4551688	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582902	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4625389	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4917705	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4917707	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4917714	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4917715	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4918960	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4918962	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4918968	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4918969	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4918974	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5014871	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6584017	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6584018	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6584022	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6584023	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6584027	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6584030	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7069030	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7071836	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7074403	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7077566	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7083411	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7083960	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7086986	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7088584	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7088961	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7094382	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7094484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7095587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7096317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7097489	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7099844	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7478595	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7893677	0.80[ASN][1000 genomes]
rs7913082	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7914286	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7921242	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]

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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1539433	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs1539433	ENTPD1	cis	multi-tissue	Pritchard
rs1539433	TCTN3	Cis_1M	lymphoblastoid	RTeQTL
rs1539433	ALDH18A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97516600-97521400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:97516800-97521200	Weak transcription	Left Ventricle	heart
3	chr10:97516800-97524800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:97517200-97520200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr10:97517200-97521200	Weak transcription	Primary T cells from cord blood	blood
6	chr10:97517200-97521400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:97517400-97519800	Enhancers	Colon Smooth Muscle	Colon
8	chr10:97517400-97520000	Weak transcription	Brain Anterior Caudate	brain
9	chr10:97517600-97523000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr10:97517600-97523600	Enhancers	Primary B cells from peripheral blood	blood
11	chr10:97518000-97519800	Enhancers	HUVEC	blood vessel
12	chr10:97518200-97519800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr10:97518400-97519800	Enhancers	Duodenum Mucosa	Duodenum
14	chr10:97518400-97521200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr10:97518600-97521200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:97518600-97521200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:97518600-97521200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr10:97518600-97534000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:97518800-97521200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr10:97518800-97521400	Enhancers	Primary B cells from cord blood	blood
21	chr10:97518800-97521400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr10:97518800-97534000	Weak transcription	Fetal Stomach	stomach
23	chr10:97519000-97519800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr10:97519000-97519800	Enhancers	Rectal Smooth Muscle	rectum
25	chr10:97519000-97520800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr10:97519200-97520000	Enhancers	Primary hematopoietic stem cells	blood
27	chr10:97519200-97520200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr10:97519200-97521200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:97519200-97521400	Weak transcription	Lung	lung
30	chr10:97519200-97521400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr10:97519200-97521600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:97519400-97519800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:97519400-97521200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr10:97519400-97521200	Weak transcription	Aorta	Aorta
35	chr10:97519400-97521200	Weak transcription	Brain Substantia Nigra	brain
36	chr10:97519400-97521200	Weak transcription	Spleen	Spleen
37	chr10:97519400-97522600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
38	chr10:97519600-97520000	Enhancers	Small Intestine	intestine
39	chr10:97519600-97521400	Enhancers	Monocytes-CD14+_RO01746	blood

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