Variant report

Variant	rs2659552
Chromosome Location	chr4:102082263-102082264
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	POLR2A	chr4:102081527-102082695	MCF10A-Er-Src	breast:	n/a	n/a
2	SP1	chr4:102082018-102082851	A549	lung:	n/a	n/a
3	CEBPB	chr4:102082137-102083236	HCT-116	colon:	n/a	chr4:102082786-102082797
4	ATF3	chr4:102082206-102082688	A549	lung:	n/a	n/a
5	TEAD4	chr4:102082186-102082572	A549	lung:	n/a	n/a
6	JUND	chr4:102082225-102082655	A549	lung:	n/a	n/a
7	GATA3	chr4:102082236-102082694	MCF-7	breast:	n/a	chr4:102082653-102082660
8	EP300	chr4:102082001-102082821	A549	lung:	n/a	chr4:102082072-102082081
9	FOSL2	chr4:102081857-102082801	A549	lung:	n/a	chr4:102082072-102082080 chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082071-102082081
10	POLR2A	chr4:102082255-102082326	MCF-7	breast:	n/a	n/a
11	JUND	chr4:102081879-102082714	HCT-116	colon:	n/a	chr4:102082072-102082080 chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082071-102082081
12	BCL3	chr4:102082143-102082701	A549	lung:	n/a	n/a
13	SRF	chr4:102082025-102083243	HCT-116	colon:	n/a	chr4:102082980-102082993 chr4:102082978-102082996
14	FOSL2	chr4:102082250-102082612	A549	lung:	n/a	n/a
15	USF1	chr4:102082232-102082630	A549	lung:	n/a	n/a
16	ATF3	chr4:102082178-102082689	A549	lung:	n/a	n/a
17	FOS	chr4:102082043-102082570	MCF10A-Er-Src	breast:	n/a	chr4:102082072-102082080 chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082071-102082081
18	GATA3	chr4:102081797-102082970	A549	lung:	n/a	chr4:102082653-102082660
19	NR3C1	chr4:102082242-102082595	A549	lung:	n/a	n/a
20	TCF12	chr4:102081887-102083043	A549	lung:	n/a	n/a
21	NR3C1	chr4:102082243-102082621	A549	lung:	n/a	n/a
22	MAX	chr4:102082187-102082638	A549	lung:	n/a	n/a
23	FOSL1	chr4:102081781-102083234	HCT-116	colon:	n/a	chr4:102082072-102082080 chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082071-102082081
24	BCL3	chr4:102081992-102082833	A549	lung:	n/a	chr4:102082071-102082080
25	FOSL1	chr4:102081786-102082679	HCT-116	colon:	n/a	chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082072-102082080 chr4:102082071-102082081
26	SP1	chr4:102081977-102082813	A549	lung:	n/a	n/a
27	MAX	chr4:102082091-102082718	A549	lung:	n/a	n/a
28	RAD21	chr4:102082224-102082588	A549	lung:	n/a	n/a
29	TCF12	chr4:102082191-102082730	A549	lung:	n/a	n/a
30	JUND	chr4:102081872-102083084	HCT-116	colon:	n/a	chr4:102082072-102082080 chr4:102082071-102082081 chr4:102082072-102082080 chr4:102082072-102082079 chr4:102082071-102082081
31	CEBPB	chr4:102082067-102082757	A549	lung:	n/a	n/a
32	FOS	chr4:102082259-102082592	MCF10A-Er-Src	breast:	n/a	n/a
33	NR3C1	chr4:102082217-102082542	A549	lung:	n/a	n/a
34	SP1	chr4:102081793-102083332	HCT-116	colon:	n/a	n/a
35	FOXA1	chr4:102082262-102082465	T-47D	breast:	n/a	n/a
36	CEBPB	chr4:102081867-102083198	HCT-116	colon:	n/a	chr4:102082786-102082797
37	NR3C1	chr4:102082226-102082635	A549	lung:	n/a	n/a
38	CEBPB	chr4:102082223-102082650	A549	lung:	n/a	n/a
39	GABPA	chr4:102082201-102082661	A549	lung:	n/a	n/a
40	FOXA2	chr4:102082153-102082787	A549	lung:	n/a	n/a
41	GATA3	chr4:102082016-102082763	A549	lung:	n/a	chr4:102082653-102082660
42	NR3C1	chr4:102082154-102082640	A549	lung:	n/a	n/a
43	FOXA2	chr4:102082263-102082721	A549	lung:	n/a	n/a
44	REST	chr4:102082110-102082666	A549	lung:	n/a	chr4:102082549-102082557
45	TEAD4	chr4:102082139-102082791	A549	lung:	n/a	n/a
46	SP1	chr4:102081864-102083202	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:102081888-102082614	HCT-116	colon:	n/a	n/a
48	EP300	chr4:102081767-102082921	A549	lung:	n/a	chr4:102082072-102082081

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102072492..102076401-chr4:102080849..102083286,3	MCF-7	breast:

Variant related genes	Relation type
PPP3CA	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10018021	0.80[EUR][1000 genomes]
rs10030389	0.81[EUR][1000 genomes]
rs10516471	0.81[EUR][1000 genomes]
rs13103902	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13111186	0.81[EUR][1000 genomes]
rs13118966	0.81[EUR][1000 genomes]
rs13125501	0.82[EUR][1000 genomes]
rs13128841	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13135924	0.81[EUR][1000 genomes]
rs13142024	0.81[EUR][1000 genomes]
rs1810024	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880943	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063058	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695215	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695219	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4590038	0.81[EUR][1000 genomes]
rs4698912	0.81[EUR][1000 genomes]
rs4698913	0.81[EUR][1000 genomes]
rs4699106	0.81[EUR][1000 genomes]
rs7677550	0.81[EUR][1000 genomes]
rs950177	0.81[EUR][1000 genomes]
rs9995338	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv18835	chr4:102081201-102084993	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv2760883	chr4:102081357-102088150	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102075400-102084200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr4:102078400-102093200	Weak transcription	HUVEC	blood vessel
4	chr4:102078400-102096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:102078600-102088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:102078600-102090200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:102078800-102084000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr4:102078800-102084000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:102078800-102084000	Weak transcription	HMEC	breast
10	chr4:102078800-102096000	Weak transcription	Ovary	ovary
11	chr4:102079000-102088800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr4:102079600-102088800	Weak transcription	Psoas Muscle	Psoas
14	chr4:102079800-102082800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:102079800-102087200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:102079800-102096400	Weak transcription	Adipose Nuclei	Adipose
17	chr4:102080000-102083000	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:102080000-102084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:102080000-102085200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:102080000-102085200	Weak transcription	Osteobl	bone
21	chr4:102080000-102092200	Weak transcription	NHDF-Ad	bronchial
22	chr4:102080000-102092600	Weak transcription	NH-A	brain
23	chr4:102080200-102085200	Weak transcription	HSMM	muscle
24	chr4:102080400-102084600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:102080400-102087400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:102080400-102088800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:102080600-102082400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:102080600-102082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:102080600-102093000	Weak transcription	NHLF	lung
30	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:102080800-102082600	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:102081000-102090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:102081200-102082600	Strong transcription	Primary B cells from cord blood	blood
34	chr4:102081400-102082800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr4:102081600-102083000	Enhancers	Brain Anterior Caudate	brain
36	chr4:102081800-102082800	Active TSS	A549	lung
37	chr4:102082000-102082800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:102082000-102082800	Enhancers	NHEK	skin
39	chr4:102082000-102083000	Enhancers	Fetal Brain Female	brain
40	chr4:102082000-102083400	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr4:102082200-102082800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr4:102082200-102083000	Enhancers	Brain Substantia Nigra	brain
43	chr4:102082200-102083200	Enhancers	Brain Angular Gyrus	brain

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