Variant report

Variant	rs7652476
Chromosome Location	chr3:52866317-52866318
allele	C/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	ZNF263	chr3:52865598-52866336	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr3:52863669-52866323	Hela-S3	cervix:	n/a	n/a
3	SMARCB1	chr3:52864407-52866488	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:
2	chr3:52803948..52806345-chr3:52865313..52866850,2	MCF-7	breast:

Variant related genes	Relation type
ITIH4	TF binding region
ENSG00000114904	Chromatin interaction
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10049313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052728	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12637566	1.00[ASN][1000 genomes]
rs13066997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052326	1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986739	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001733	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246889	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276820	1.00[ASN][1000 genomes]
rs2276821	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336157	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336556	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535615	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535617	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2535618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535620	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535621	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535631	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535632	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535641	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535643	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2535644	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2535645	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535646	1.00[EUR][1000 genomes];1.00[ASN][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]
rs2590841	1.00[EUR][1000 genomes]
rs2710315	1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710325	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710341	1.00[ASN][1000 genomes]
rs2710343	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878633	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878634	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878636	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34352685	0.89[ASN][1000 genomes]
rs3774361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234635	1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs4234637	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687557	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687666	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687668	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687669	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687671	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687674	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	1.00[EUR][1000 genomes]
rs6445540	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6791937	0.91[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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638431	0.93[AFR][1000 genomes]
rs7645169	0.95[AFR][1000 genomes]
rs7647534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649515	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs9681089	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682449	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9877711	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
2	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
10	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52858400-52866800	Weak transcription	Fetal Brain Female	brain
14	chr3:52858400-52867200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:52858600-52866800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52858600-52867000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:52858800-52866800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:52861200-52866400	Weak transcription	Primary T cells from cord blood	blood
25	chr3:52861200-52868800	Weak transcription	Lung	lung
26	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:52864000-52866400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:52864400-52866400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:52864400-52866400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:52864400-52866600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:52864400-52866600	Enhancers	NHLF	lung
34	chr3:52864400-52867200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:52864600-52866600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr3:52864600-52866800	Enhancers	HSMMtube	muscle
38	chr3:52864600-52867000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52864600-52867400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:52864800-52866400	Enhancers	Right Ventricle	heart
41	chr3:52864800-52866600	Enhancers	Aorta	Aorta
42	chr3:52864800-52866600	Enhancers	HSMM	muscle
43	chr3:52864800-52867000	Weak transcription	Thymus	Thymus
44	chr3:52865000-52866400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:52865000-52866600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:52865000-52866600	Enhancers	NHDF-Ad	bronchial
47	chr3:52865000-52866800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:52865000-52867200	Genic enhancers	Fetal Muscle Leg	muscle
49	chr3:52865000-52867800	Enhancers	Psoas Muscle	Psoas
50	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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