Variant report

Variant	rs7629528
Chromosome Location	chr3:52878825-52878826
allele	A/C
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	SPI1	chr3:52878424-52879038	HL-60	blood:	n/a	n/a
2	SPI1	chr3:52878577-52879021	HL-60	blood:	n/a	n/a
3	POLR2A	chr3:52878267-52878848	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
TMEM110	TF binding region
TMEM110-MUSTN1	TF binding region

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10049313	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052728	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486028	1.00[EUR][1000 genomes]
rs13066997	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001733	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336155	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336157	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2336556	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535617	0.97[AFR][1000 genomes]
rs2535618	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535643	0.91[AMR][1000 genomes]
rs2535644	0.91[AMR][1000 genomes]
rs2535645	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[EUR][1000 genomes]
rs2564946	1.00[EUR][1000 genomes]
rs2577828	1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2581814	1.00[EUR][1000 genomes]
rs2590840	1.00[EUR][1000 genomes]
rs2710315	1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710318	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710343	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	1.00[AMR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs7623667	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7637212	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638431	0.95[AFR][1000 genomes]
rs7645169	0.97[AFR][1000 genomes]
rs7647534	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	1.00[AMR][1000 genomes];1.00[EUR][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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52866000-52884800	Weak transcription	HMEC	breast
4	chr3:52866200-52885200	Weak transcription	NHEK	skin
5	chr3:52866600-52879200	Weak transcription	Osteobl	bone
6	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
7	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
11	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
12	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
17	chr3:52870600-52879400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52871200-52879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:52872600-52879000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:52873400-52879600	Weak transcription	GM12878-XiMat	blood
21	chr3:52873400-52891600	Strong transcription	Primary T cells from cord blood	blood
22	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:52873600-52881800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:52873600-52882600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:52873600-52889000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:52873800-52882200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:52873800-52889000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:52873800-52891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:52874200-52879600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:52874200-52883800	Enhancers	Psoas Muscle	Psoas
31	chr3:52874400-52879800	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr3:52874600-52879000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:52874800-52880200	Enhancers	Right Atrium	heart
34	chr3:52875200-52879400	Weak transcription	HSMM	muscle
35	chr3:52875600-52880200	Enhancers	HSMMtube	muscle
36	chr3:52875800-52882600	Weak transcription	NH-A	brain
37	chr3:52875800-52885800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:52876000-52885800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:52876400-52879600	Genic enhancers	Primary monocytes fromperipheralblood	blood
40	chr3:52876400-52880000	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:52876600-52880000	Genic enhancers	Fetal Stomach	stomach
42	chr3:52876600-52880400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:52876600-52881200	Weak transcription	Fetal Intestine Large	intestine
44	chr3:52876800-52879400	Weak transcription	Brain Anterior Caudate	brain
45	chr3:52876800-52879400	Weak transcription	NHLF	lung
46	chr3:52876800-52879800	Enhancers	Placenta	Placenta
47	chr3:52876800-52880400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr3:52876800-52881400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:52876800-52881600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:52876800-52881600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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