Variant report

Variant	rs635690
Chromosome Location	chr15:42448869-42448870
allele	C/T
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	CEBPB	chr15:42448766-42448895	Hela-S3	cervix:	n/a	n/a
2	ELF1	chr15:42447982-42449265	MCF-7	breast:	n/a	chr15:42448908-42448921
3	GATA3	chr15:42448624-42448892	T-47D	breast:	n/a	n/a
4	CTCF	chr15:42448820-42448970	WERI-Rb-1	eye:	n/a	n/a
5	RAD21	chr15:42448545-42448965	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr15:42448549-42449001	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr15:42448730-42449122	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr15:42448720-42448870	HEEpiC	esophagus:	n/a	n/a
9	MAX	chr15:42448545-42448968	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr15:42448780-42448930	BE2_C	brain:	n/a	n/a
11	MAFK	chr15:42448727-42448878	HepG2	liver:	n/a	chr15:42448802-42448817
12	POLR2A	chr15:42448629-42449015	MCF-7	breast:	n/a	n/a
13	GATA3	chr15:42447857-42449035	MCF-7	breast:	n/a	chr15:42448301-42448322
14	SIN3AK20	chr15:42447871-42449237	MCF-7	breast:	n/a	n/a
15	POLR2A	chr15:42448634-42448966	MCF-7	breast:	n/a	n/a
16	FOXA1	chr15:42448678-42448974	T-47D	breast:	n/a	n/a
17	ELF1	chr15:42448762-42449040	K562	blood:	n/a	chr15:42448908-42448921

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42448110..42450231-chr15:42456166..42458018,2	MCF-7	breast:

Variant related genes	Relation type
PLA2G4F	TF binding region
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10152909	0.86[ASN][1000 genomes]
rs11070363	0.86[ASN][1000 genomes]
rs12324804	0.86[ASN][1000 genomes]
rs12440779	0.82[ASN][1000 genomes]
rs12442769	0.86[ASN][1000 genomes]
rs12915387	0.90[ASN][1000 genomes]
rs12915946	0.86[ASN][1000 genomes]
rs12917071	0.86[ASN][1000 genomes]
rs1616957	0.94[ASN][1000 genomes]
rs1619537	0.94[ASN][1000 genomes]
rs1626437	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1630294	0.90[ASN][1000 genomes]
rs1678987	0.90[ASN][1000 genomes]
rs1678988	0.90[ASN][1000 genomes]
rs1678989	0.90[ASN][1000 genomes]
rs1678990	0.90[ASN][1000 genomes]
rs1678995	1.00[ASN][1000 genomes]
rs1678996	1.00[ASN][1000 genomes]
rs1679000	1.00[ASN][1000 genomes]
rs1679001	0.98[ASN][1000 genomes]
rs1679008	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1679011	0.86[ASN][1000 genomes]
rs1703748	1.00[ASN][1000 genomes]
rs1703751	0.96[ASN][1000 genomes]
rs1703753	0.98[ASN][1000 genomes]
rs1712390	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1712391	0.98[ASN][1000 genomes]
rs1712397	0.94[ASN][1000 genomes]
rs1712406	0.94[ASN][1000 genomes]
rs1712407	0.98[ASN][1000 genomes]
rs1712408	0.86[ASN][1000 genomes]
rs1712409	0.86[ASN][1000 genomes]
rs1712410	0.86[ASN][1000 genomes]
rs1712417	0.90[ASN][1000 genomes]
rs1712420	0.90[ASN][1000 genomes]
rs1712422	0.94[ASN][1000 genomes]
rs1712442	0.94[ASN][1000 genomes]
rs2412671	1.00[ASN][1000 genomes]
rs2412674	0.94[ASN][1000 genomes]
rs2620378	1.00[ASN][1000 genomes]
rs2620379	0.98[ASN][1000 genomes]
rs2620380	1.00[ASN][1000 genomes]
rs2620381	0.92[ASN][1000 genomes]
rs2620383	0.94[ASN][1000 genomes]
rs2620387	0.86[ASN][1000 genomes]
rs2663092	1.00[ASN][1000 genomes]
rs2663096	0.94[ASN][1000 genomes]
rs2677751	1.00[ASN][1000 genomes]
rs28767320	0.94[ASN][1000 genomes]
rs2928333	0.98[ASN][1000 genomes]
rs4923934	0.86[ASN][1000 genomes]
rs4924633	0.90[ASN][1000 genomes]
rs4924635	0.86[ASN][1000 genomes]
rs4924636	0.90[ASN][1000 genomes]
rs4924638	0.86[ASN][1000 genomes]
rs583541	0.96[ASN][1000 genomes]
rs588695	0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs590540	0.98[ASN][1000 genomes]
rs593910	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs598441	0.96[ASN][1000 genomes]
rs599316	0.82[ASN][1000 genomes]
rs602270	1.00[ASN][1000 genomes]
rs603468	0.94[ASN][1000 genomes]
rs607959	0.94[ASN][1000 genomes]
rs609660	0.96[ASN][1000 genomes]
rs613090	0.94[ASN][1000 genomes]
rs613131	0.96[ASN][1000 genomes]
rs613157	1.00[ASN][1000 genomes]
rs614733	1.00[ASN][1000 genomes]
rs614774	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs615023	0.98[ASN][1000 genomes]
rs616071	1.00[ASN][1000 genomes]
rs618161	0.94[ASN][1000 genomes]
rs621365	1.00[ASN][1000 genomes]
rs627478	1.00[ASN][1000 genomes]
rs629255	1.00[ASN][1000 genomes]
rs633310	0.90[ASN][1000 genomes]
rs633483	0.98[ASN][1000 genomes]
rs635617	0.98[ASN][1000 genomes]
rs635669	1.00[ASN][1000 genomes]
rs635919	0.98[ASN][1000 genomes]
rs636604	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637445	1.00[ASN][1000 genomes]
rs638240	0.94[ASN][1000 genomes]
rs641119	0.98[ASN][1000 genomes]
rs644627	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs645304	1.00[ASN][1000 genomes]
rs647581	0.98[ASN][1000 genomes]
rs648720	0.96[ASN][1000 genomes]
rs650910	1.00[ASN][1000 genomes]
rs652192	0.94[ASN][1000 genomes]
rs659354	0.94[ASN][1000 genomes]
rs660033	0.98[ASN][1000 genomes]
rs663454	0.98[ASN][1000 genomes]
rs665262	1.00[ASN][1000 genomes]
rs665718	1.00[ASN][1000 genomes]
rs668973	1.00[ASN][1000 genomes]
rs670329	1.00[ASN][1000 genomes]
rs670421	1.00[ASN][1000 genomes]
rs672946	1.00[ASN][1000 genomes]
rs677845	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs677895	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs683227	0.94[ASN][1000 genomes]
rs683579	0.94[ASN][1000 genomes]
rs685521	0.98[ASN][1000 genomes]
rs7181577	0.98[ASN][1000 genomes]
rs8023923	0.94[ASN][1000 genomes]
rs8030650	0.86[ASN][1000 genomes]
rs8031735	0.90[ASN][1000 genomes]
rs8036917	0.86[ASN][1000 genomes]
rs8108	0.94[ASN][1000 genomes]
rs9783720	0.86[ASN][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv9245	chr15:42441849-42453572	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv3361173	chr15:42445160-42449558	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42436000-42452000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:42439400-42451200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:42439400-42451800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:42441200-42450600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:42441800-42451000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:42444000-42451600	Weak transcription	HUVEC	blood vessel
7	chr15:42444400-42450400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:42444600-42450200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:42444800-42449800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:42444800-42450200	Weak transcription	Brain Substantia Nigra	brain
11	chr15:42444800-42450200	Weak transcription	HSMM	muscle
12	chr15:42444800-42450600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:42444800-42450600	Weak transcription	Brain Germinal Matrix	brain
14	chr15:42444800-42451000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:42444800-42451000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:42444800-42451200	Weak transcription	Aorta	Aorta
17	chr15:42445000-42449800	Weak transcription	Brain Anterior Caudate	brain
18	chr15:42445000-42450000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:42445000-42450000	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:42445000-42450200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:42445000-42451400	Weak transcription	Brain Angular Gyrus	brain
22	chr15:42445400-42451000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:42445400-42451000	Weak transcription	Right Atrium	heart
24	chr15:42445600-42449000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:42445800-42450200	Weak transcription	Psoas Muscle	Psoas
26	chr15:42446000-42450000	Enhancers	Right Ventricle	heart
27	chr15:42446000-42451000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:42446200-42449400	Enhancers	Left Ventricle	heart
29	chr15:42446600-42450400	Enhancers	Fetal Thymus	thymus
30	chr15:42446600-42451200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:42447000-42449200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:42447200-42449200	Enhancers	Pancreas	Pancrea
33	chr15:42447600-42449000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:42447600-42449000	Enhancers	Fetal Muscle Leg	muscle
35	chr15:42447600-42450400	Enhancers	Fetal Heart	heart
36	chr15:42447600-42451000	Weak transcription	Adipose Nuclei	Adipose
37	chr15:42447600-42451000	Weak transcription	Spleen	Spleen
38	chr15:42447800-42449000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:42447800-42449200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:42447800-42451400	Weak transcription	Fetal Lung	lung
41	chr15:42448000-42449000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:42448000-42449000	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr15:42448000-42449200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr15:42448000-42449600	Weak transcription	Fetal Brain Female	brain
45	chr15:42448200-42449000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr15:42448200-42449000	Enhancers	Thymus	Thymus
47	chr15:42448200-42449000	Enhancers	HSMMtube	muscle
48	chr15:42448200-42449000	Enhancers	K562	blood
49	chr15:42448200-42449200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr15:42448200-42451000	Weak transcription	Stomach Smooth Muscle	stomach

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