Variant report

Variant	rs1052728
Chromosome Location	chr3:52854472-52854473
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	CTCF	chr3:52854340-52854490	HPF	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52847640..52851112-chr3:52852588..52855076,3	MCF-7	breast:
2	chr3:52836954..52839305-chr3:52853241..52854782,2	K562	blood:
3	chr3:52462640..52463186-chr3:52854147..52854995,2	K562	blood:

Variant related genes	Relation type
ITIH4	TF binding region
ITIH4-AS1	TF binding region
ENSG00000162267	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10049313	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13066997	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17052326	1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs1986738	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001733	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336155	0.82[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	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.91[AMR][1000 genomes]
rs2336556	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535617	0.86[AFR][1000 genomes]
rs2535618	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535638	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535643	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2535644	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2535645	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535646	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]
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	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	0.86[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	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	0.82[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	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.86[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	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687659	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	0.82[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	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	0.83[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	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	0.83[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	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645169	0.80[AFR][1000 genomes]
rs7647534	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	0.83[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:7 , 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
7	nsv590308	chr3:52854335-52860806	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
6	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
7	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:52847200-52861200	Genic enhancers	Liver	Liver
9	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
11	chr3:52847800-52854600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:52848400-52865800	Weak transcription	Ovary	ovary
13	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
14	chr3:52850600-52857800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
16	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
17	chr3:52851000-52856800	Weak transcription	Fetal Brain Female	brain
18	chr3:52851200-52855400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:52851800-52855200	Strong transcription	Brain Anterior Caudate	brain
21	chr3:52851800-52856800	Weak transcription	Lung	lung
22	chr3:52851800-52858000	Weak transcription	Placenta	Placenta
23	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:52852800-52854800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
26	chr3:52853000-52857000	Weak transcription	Gastric	stomach
27	chr3:52853000-52857000	Enhancers	HepG2	liver
28	chr3:52853000-52857000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:52853000-52858400	Strong transcription	Brain Angular Gyrus	brain
30	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:52853200-52855600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr3:52853200-52859400	Strong transcription	Thymus	Thymus
33	chr3:52853400-52856600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:52853400-52857600	Strong transcription	Spleen	Spleen
35	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:52853600-52854800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr3:52853600-52855200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:52853600-52855600	Enhancers	Fetal Muscle Trunk	muscle
39	chr3:52853800-52855000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:52853800-52855800	Strong transcription	Right Ventricle	heart
41	chr3:52854000-52854800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:52854000-52856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:52854000-52858800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:52854000-52859000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:52854000-52861200	Strong transcription	Pancreas	Pancrea
46	chr3:52854200-52855200	Strong transcription	Brain Substantia Nigra	brain
47	chr3:52854200-52855600	Strong transcription	Fetal Thymus	thymus
48	chr3:52854200-52859000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:52854400-52854800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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