Variant report

Variant	rs3797997
Chromosome Location	chr5:9361811-9361812
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	RAD21	chr5:9361786-9362287	ECC-1	luminal epithelium:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362182-9362194
2	IRF4	chr5:9361760-9362439	GM12878	blood:	n/a	n/a
3	RAD21	chr5:9361728-9362610	SK-N-SH	brain:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362420-9362430 chr5:9362182-9362194
4	MTA3	chr5:9361778-9364108	GM12878	blood:	n/a	n/a
5	CTCF	chr5:9361680-9361830	GM06990	blood:	n/a	n/a
6	STAT3	chr5:9361654-9361831	MCF10A-Er-Src	breast:	n/a	chr5:9361669-9361677
7	MYC	chr5:9361750-9362172	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr5:9361796-9362260	H1-hESC	embryonic stem cell:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362182-9362194
9	PML	chr5:9361803-9362538	GM12878	blood:	n/a	n/a
10	BCLAF1	chr5:9361799-9363834	GM12878	blood:	n/a	n/a
11	CTCF	chr5:9361607-9362466	SK-N-SH	brain:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
12	RAD21	chr5:9361807-9362245	SK-N-SH_RA	brain:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362182-9362194
13	STAT5A	chr5:9361807-9362406	GM12878	blood:	n/a	n/a
14	CTCF	chr5:9361786-9362408	H1-hESC	embryonic stem cell:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
15	CTCF	chr5:9361810-9362248	A549	lung:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
16	RAD21	chr5:9361750-9362369	MCF-7	breast:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362182-9362194
17	CTCF	chr5:9361754-9362342	MCF-7	breast:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
18	CTCF	chr5:9361667-9362439	A549	lung:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
19	FOXM1	chr5:9361704-9363949	GM12878	blood:	n/a	n/a
20	ATF2	chr5:9361779-9363766	GM12878	blood:	n/a	n/a
21	SMC3	chr5:9361561-9362424	SK-N-SH	brain:	n/a	chr5:9362042-9362056
22	EBF1	chr5:9361702-9363348	GM12878	blood:	n/a	chr5:9362666-9362676
23	CTCF	chr5:9361743-9362407	MCF-7	breast:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
24	FOXM1	chr5:9361777-9363664	GM12878	blood:	n/a	n/a
25	NFIC	chr5:9361810-9363765	GM12878	blood:	n/a	n/a
26	RAD21	chr5:9361786-9362310	H1-hESC	embryonic stem cell:	n/a	chr5:9362045-9362054 chr5:9362041-9362060 chr5:9362182-9362194
27	CTCF	chr5:9361787-9362269	HepG2	liver:	n/a	chr5:9362045-9362053 chr5:9362040-9362058 chr5:9362042-9362063 chr5:9362041-9362057 chr5:9362085-9362094
28	FOXA2	chr5:9361729-9362271	A549	lung:	n/a	n/a
29	RUNX3	chr5:9361808-9363843	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:9361518..9362621-chr5:9498467..9499687,7	MCF-7	breast:
2	chr5:9361718..9362331-chr5:9617304..9617828,2	MCF-7	breast:
3	chr5:9361534..9362572-chr5:9498705..9499722,10	MCF-7	breast:
4	chr5:9361657..9362168-chr5:9514121..9514726,2	MCF-7	breast:
5	chr5:9361616..9362826-chr5:9543590..9545181,8	MCF-7	breast:
6	chr5:9361570..9362507-chr5:9388042..9388595,2	MCF-7	breast:
7	chr5:9361538..9362121-chr5:9514076..9514589,2	MCF-7	breast:
8	chr5:9361687..9362730-chr5:9617093..9618979,9	MCF-7	breast:
9	chr5:9361677..9362185-chr5:9618283..9619251,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248537	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10462867	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1205715	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1205724	0.85[ASN][1000 genomes]
rs13355242	0.86[EUR][1000 genomes]
rs16882400	1.00[EUR][1000 genomes]
rs16882463	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16882519	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797983	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797993	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797999	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798000	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60031337	1.00[EUR][1000 genomes]
rs73742654	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7702342	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9332800-9372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:9347000-9365600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:9355200-9370200	Weak transcription	Pancreas	Pancrea
4	chr5:9357200-9377800	Weak transcription	Fetal Intestine Large	intestine
5	chr5:9357800-9363200	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:9357800-9365800	Weak transcription	Brain Germinal Matrix	brain
7	chr5:9358000-9389400	Weak transcription	Brain Substantia Nigra	brain
8	chr5:9358600-9362000	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:9358800-9363400	Weak transcription	Fetal Stomach	stomach
10	chr5:9358800-9369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:9358800-9372400	Weak transcription	Fetal Intestine Small	intestine
12	chr5:9359200-9365800	Weak transcription	Left Ventricle	heart
13	chr5:9359200-9382800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:9359400-9362400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:9359400-9363400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:9359600-9363800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:9359600-9372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:9359800-9363200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:9359800-9363200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:9359800-9363400	Weak transcription	NHDF-Ad	bronchial
21	chr5:9359800-9372400	Weak transcription	Fetal Kidney	kidney
22	chr5:9360000-9362000	Weak transcription	Osteobl	bone
23	chr5:9360000-9362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:9360000-9363400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:9360200-9363000	Weak transcription	NH-A	brain
26	chr5:9360200-9363400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:9360400-9362000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:9360400-9362200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:9360400-9363000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:9360400-9363000	Weak transcription	Fetal Heart	heart
31	chr5:9360400-9363000	Weak transcription	NHLF	lung
32	chr5:9360400-9370200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:9361600-9362000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:9361600-9362000	Flanking Active TSS	GM12878-XiMat	blood
35	chr5:9361600-9362400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:9361800-9362000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:9361800-9362400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:9361800-9362600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:9361800-9363600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:9361800-9364000	Enhancers	Placenta Amnion	Placenta Amnion

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