Variant report

Variant	rs16955734
Chromosome Location	chr15:30040233-30040234
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	chr15:30040170-30040319	Hela-S3	cervix:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
2	CTCF	chr15:30040180-30040330	GM12864	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
3	CTCF	chr15:30040045-30040366	A549	lung:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
4	SMC3	chr15:30040018-30040637	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr15:30040120-30040270	HCM	heart:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
6	RAD21	chr15:30039954-30040546	HCT-116	colon:	n/a	chr15:30040236-30040255
7	RAD21	chr15:30039999-30040444	HepG2	liver:	n/a	chr15:30040236-30040255
8	CTCF	chr15:30040100-30040250	GM12873	blood:	n/a	n/a
9	CTCF	chr15:30040100-30040250	HRE	kidney:	n/a	n/a
10	CTCF	chr15:30040160-30040310	AoAF	blood vessel:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
11	CTCF	chr15:30040130-30040343	Pancreas_OC	pancreas:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
12	CTCF	chr15:30040180-30040330	HCFaa	heart:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
13	CTCF	chr15:30040120-30040270	HUVEC	blood vessel:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
14	CTCF	chr15:30040100-30040250	SAEC	small airway:	n/a	n/a
15	CTCF	chr15:30040120-30040270	HPAF	blood vessel:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
16	CTCF	chr15:30040174-30040306	GM10266	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
17	SMC3	chr15:30040085-30040613	GM12878	blood:	n/a	n/a
18	CTCF	chr15:30040160-30040310	Hela-S3	cervix:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
19	CTCF	chr15:30040160-30040310	HRE	kidney:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
20	RAD21	chr15:30039899-30040590	A549	lung:	n/a	chr15:30040236-30040255
21	CTCF	chr15:30040140-30040290	HA-sp	spinal cord:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
22	CTCF	chr15:30040120-30040270	HEEpiC	esophagus:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
23	CTCF	chr15:30040103-30040367	HUVEC	blood vessel:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
24	CTCF	chr15:30040160-30040310	HMEC	breast:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
25	CTCF	chr15:30040120-30040270	AG09309	skin:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
26	MYC	chr15:30040122-30040427	MCF10A-Er-Src	breast:	n/a	n/a
27	RAD21	chr15:30040000-30040521	ECC-1	luminal epithelium:	n/a	chr15:30040236-30040255
28	CTCF	chr15:30039949-30040447	A549	lung:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
29	CTCF	chr15:30040027-30040357	K562	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
30	CTCF	chr15:30040140-30040290	AG10803	skin:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
31	CTCF	chr15:30040164-30040284	GM20000	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
32	CTCF	chr15:30040180-30040330	HPAF	blood vessel:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
33	CTCF	chr15:30040160-30040310	AG04450	lung:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
34	RAD21	chr15:30040104-30040324	K562	blood:	n/a	chr15:30040236-30040255
35	RAD21	chr15:30040054-30040435	GM12878	blood:	n/a	chr15:30040236-30040255
36	CTCF	chr15:30040140-30040290	AG09319	gingival:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
37	CTCF	chr15:30040140-30040290	AG04449	skin:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
38	RFX5	chr15:30040080-30040397	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr15:30040146-30040278	LNCaP	prostate:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
40	CTCF	chr15:30039797-30040778	SK-N-SH	brain:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
41	RAD21	chr15:30040152-30040319	K562	blood:	n/a	chr15:30040236-30040255
42	CTCF	chr15:30040193-30040282	Kidney_OC	kidney:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
43	CTCF	chr15:30040180-30040330	GM12872	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
44	ZNF143	chr15:30040072-30040410	GM12878	blood:	n/a	n/a
45	CTCF	chr15:30040057-30040449	K562	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
46	CTCF	chr15:30040200-30040350	AG04449	skin:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
47	RAD21	chr15:30039978-30040482	A549	lung:	n/a	chr15:30040236-30040255
48	CTCF	chr15:30040120-30040270	HL-60	blood:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
49	CTCF	chr15:30040192-30040312	LNCaP	prostate:	n/a	chr15:30040237-30040258 chr15:30040235-30040253
50	CTCF	chr15:30039787-30040837	A549	lung:	n/a	chr15:30040237-30040258 chr15:30040235-30040253

No.	Distal block	Cell Line	Cell type
1	chr15:30040202..30040753-chr15:30227652..30228190,3	MCF-7	breast:
2	chr15:30038685..30041950-chr15:30111747..30114344,3	K562	blood:
3	chr15:30039757..30041000-chr15:30217656..30218757,7	MCF-7	breast:
4	chr15:30038243..30040295-chr15:30113085..30115375,2	MCF-7	breast:
5	chr15:30039776..30040422-chr15:30217833..30218539,2	K562	blood:
6	chr15:30039724..30040629-chr15:30367249..30368123,2	K562	blood:

Variant related genes	Relation type
TJP1	TF binding region
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16954392	0.95[AFR][1000 genomes]
rs2293185	0.85[YRI][hapmap];0.95[AFR][1000 genomes]
rs28461632	1.00[LWK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs28729338	0.95[AFR][1000 genomes]
rs36012099	1.00[AFR][1000 genomes]
rs45456792	0.86[AFR][1000 genomes]
rs45611333	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking 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 target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30016600-30052000	Weak transcription	Spleen	Spleen
2	chr15:30016600-30068200	Weak transcription	Brain Germinal Matrix	brain
3	chr15:30017600-30041600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:30017600-30048600	Weak transcription	Fetal Brain Male	brain
5	chr15:30018200-30052000	Weak transcription	Gastric	stomach
6	chr15:30021200-30061600	Weak transcription	Colonic Mucosa	Colon
7	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
8	chr15:30025200-30065000	Weak transcription	Fetal Brain Female	brain
9	chr15:30025800-30043200	Weak transcription	NHLF	lung
10	chr15:30026000-30051800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:30026000-30057600	Weak transcription	Esophagus	oesophagus
12	chr15:30028200-30047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:30028200-30049200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:30029200-30041800	Weak transcription	Right Ventricle	heart
15	chr15:30029600-30041600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:30029600-30048600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:30029800-30056000	Weak transcription	K562	blood
18	chr15:30030400-30060800	Weak transcription	Hela-S3	cervix
19	chr15:30030400-30067000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:30031600-30040400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:30031600-30041600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:30031600-30041600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:30031600-30046200	Weak transcription	Fetal Kidney	kidney
24	chr15:30031800-30041600	Weak transcription	HepG2	liver
25	chr15:30032800-30046400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr15:30033200-30041600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:30033200-30046600	Weak transcription	NH-A	brain
28	chr15:30033200-30051800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:30033400-30041600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:30033600-30049000	Weak transcription	HUVEC	blood vessel
31	chr15:30034200-30051400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:30034400-30041000	Weak transcription	Ovary	ovary
33	chr15:30034400-30041400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:30034400-30041600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:30034400-30041600	Weak transcription	Lung	lung
36	chr15:30034400-30041600	Weak transcription	Pancreas	Pancrea
37	chr15:30034400-30048400	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:30034400-30051800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:30034400-30051800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:30034400-30057800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:30034600-30041400	Weak transcription	Fetal Stomach	stomach
42	chr15:30034800-30040800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:30034800-30041200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:30034800-30041400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:30034800-30041400	Weak transcription	Fetal Lung	lung
46	chr15:30034800-30041400	Weak transcription	HMEC	breast
47	chr15:30034800-30041800	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:30034800-30046400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:30034800-30052800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:30035000-30040400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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