Variant report

Variant	rs2535638
Chromosome Location	chr3:52864092-52864093
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	STAT3	chr3:52864078-52865245	MCF10A-Er-Src	breast:	n/a	chr3:52864754-52864762 chr3:52865071-52865080 chr3:52865065-52865085 chr3:52864751-52864765 chr3:52865070-52865079 chr3:52865065-52865085 chr3:52865071-52865079 chr3:52864752-52864763
2	POLR2A	chr3:52863669-52866323	Hela-S3	cervix:	n/a	n/a
3	FOS	chr3:52864081-52865002	MCF10A-Er-Src	breast:	n/a	chr3:52864802-52864811
4	MAFK	chr3:52864092-52864455	HepG2	liver:	n/a	chr3:52864269-52864284

No.	Distal block	Cell Line	Cell type
1	chr3:52860455..52862109-chr3:52862343..52864733,2	K562	blood:
2	chr3:52859743..52862109-chr3:52863233..52865763,2	K562	blood:
3	chr3:52864085..52867017-chr3:52872869..52875445,2	MCF-7	breast:
4	chr3:52863659..52864274-chr6:31619900..31620694,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITIH4-1	chr3:52863876-52864686	NONHSAT089968

Variant related genes	Relation type
ITIH4	TF binding region
ENSG00000204463	Chromatin interaction
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10049313	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1052728	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13066997	0.95[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	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1986739	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001733	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001734	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245536	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246888	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246889	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256728	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2256734	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276814	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276819	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2276821	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336155	0.94[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	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336159	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336546	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2336556	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336557	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2336559	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535615	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535616	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535617	0.98[AFR][1000 genomes]
rs2535618	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535619	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535620	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535621	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535622	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535623	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535628	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535631	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535632	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535636	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535637	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535639	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535641	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2535642	0.98[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	0.90[AFR][1000 genomes];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]
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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710319	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710320	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710321	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710324	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710325	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2710327	1.00[EUR][1000 genomes]
rs2710328	0.86[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	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878633	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2878634	0.94[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	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3774361	0.98[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	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	0.90[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	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687661	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687665	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687666	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687667	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687668	0.94[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	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687671	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687674	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687675	0.95[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445542	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	0.95[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	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629350	1.00[EUR][1000 genomes]
rs7629528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637212	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638431	0.90[AFR][1000 genomes]
rs7645169	0.92[AFR][1000 genomes]
rs7647534	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649515	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650966	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9681089	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682449	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9682819	0.95[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: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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52848400-52865800	Weak transcription	Ovary	ovary
3	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
4	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
6	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:52855200-52865400	Weak transcription	Brain Substantia Nigra	brain
13	chr3:52855600-52865400	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:52856000-52865400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
16	chr3:52856200-52865600	Weak transcription	Left Ventricle	heart
17	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
18	chr3:52856600-52864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:52857800-52865400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:52858200-52865400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:52858400-52865400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52858400-52865400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:52858400-52866800	Weak transcription	Fetal Brain Female	brain
27	chr3:52858400-52867200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:52858600-52864600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:52858600-52864800	Weak transcription	Right Ventricle	heart
31	chr3:52858600-52865600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:52858600-52866800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:52858600-52867000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:52858800-52864400	Weak transcription	Placenta	Placenta
35	chr3:52858800-52866800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52859000-52865200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:52859200-52865400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
43	chr3:52860400-52865400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52861000-52865000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:52861200-52865600	Weak transcription	Esophagus	oesophagus
46	chr3:52861200-52866400	Weak transcription	Primary T cells from cord blood	blood
47	chr3:52861200-52868800	Weak transcription	Lung	lung
48	chr3:52861600-52864200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:52861600-52865000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:52861800-52865400	Weak transcription	Spleen	Spleen

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