Variant report

Variant	rs16966424
Chromosome Location	chr15:45005933-45005934
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:162)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:162 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45002354-45013577	GM18951	blood:	n/a	n/a
2	STAT5A	chr15:45005546-45006066	GM12878	blood:	n/a	chr15:45005880-45005888
3	CTCF	chr15:45005920-45006070	GM12868	blood:	n/a	n/a
4	CTCF	chr15:45005860-45006010	NB4	blood:	n/a	n/a
5	POLR2A	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:45005511-45010190	GM12891	blood:	n/a	n/a
7	RAD21	chr15:45005848-45006202	IMR90	lung:	n/a	n/a
8	CTCF	chr15:45005842-45006203	K562	blood:	n/a	n/a
9	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
10	CTCF	chr15:45005922-45006118	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr15:45005922-45006130	HepG2	liver:	n/a	n/a
12	CTCF	chr15:45005900-45006050	GM12864	blood:	n/a	n/a
13	ARID3A	chr15:45005601-45006191	K562	blood:	n/a	n/a
14	CTCF	chr15:45005612-45006271	A549	lung:	n/a	n/a
15	RAD21	chr15:45005859-45006224	HepG2	liver:	n/a	n/a
16	SMC3	chr15:45005722-45006300	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
18	CTCF	chr15:45005877-45006174	MCF-7	breast:	n/a	n/a
19	RAD21	chr15:45005853-45006289	A549	lung:	n/a	n/a
20	POLR2A	chr15:45005695-45007424	A549	lung:	n/a	n/a
21	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
22	CTCF	chr15:45005840-45005990	HVMF	connective:	n/a	n/a
23	RAD21	chr15:45005749-45006292	A549	lung:	n/a	n/a
24	RAD21	chr15:45005757-45006324	MCF-7	breast:	n/a	n/a
25	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
26	POLR2A	chr15:45005569-45006188	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
28	SMC3	chr15:45005301-45006603	GM12878	blood:	n/a	n/a
29	BCLAF1	chr15:45005533-45006660	GM12878	blood:	n/a	n/a
30	CTCF	chr15:45005900-45006050	AG10803	skin:	n/a	n/a
31	POLR2A	chr15:45005722-45006696	HL-60	blood:	n/a	n/a
32	CTCF	chr15:45005840-45005990	A549	lung:	n/a	n/a
33	RAD21	chr15:45005751-45006204	HCT-116	colon:	n/a	n/a
34	CTCF	chr15:45005900-45006050	HAc	cerebellar:	n/a	n/a
35	CTCF	chr15:45005900-45006050	AG09309	skin:	n/a	n/a
36	USF2	chr15:45005923-45006057	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr15:45005920-45006070	K562	blood:	n/a	n/a
38	CTCF	chr15:45005839-45006241	K562	blood:	n/a	n/a
39	POLR2A	chr15:45002322-45013693	GM19193	blood:	n/a	n/a
40	CTCF	chr15:45005920-45006070	HMF	breast:	n/a	n/a
41	CTCF	chr15:45005920-45006070	HPF	lung:	n/a	n/a
42	CTCF	chr15:45005920-45006070	AG10803	skin:	n/a	n/a
43	RAD21	chr15:45005767-45006170	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr15:45005791-45006214	MCF-7	breast:	n/a	n/a
45	POLR2A	chr15:45002192-45013674	GM12891	blood:	n/a	n/a
46	CTCF	chr15:45005917-45006114	HUVEC	blood vessel:	n/a	n/a
47	SMC3	chr15:45005823-45006272	K562	blood:	n/a	n/a
48	CTCF	chr15:45005880-45006030	HCFaa	heart:	n/a	n/a
49	CTCF	chr15:45005761-45006203	A549	lung:	n/a	n/a
50	RAD21	chr15:45005794-45006236	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:21112938..21114460-chr15:45004450..45006409,2	K562	blood:
2	chr15:45004559..45007244-chr15:45019568..45021417,3	MCF-7	breast:
3	chr15:45005716..45006437-chr15:45076991..45077613,2	MCF-7	breast:
4	chr15:44951739..44957508-chr15:45000588..45008057,33	K562	blood:
5	chr15:44980888..44990623-chr15:45002366..45006726,14	K562	blood:
6	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
7	chr15:45005587..45006311-chr15:45030339..45030895,2	MCF-7	breast:
8	chr15:44968819..44972092-chr15:45002551..45007992,5	K562	blood:
9	chr15:45005533..45006393-chr15:45030225..45030830,2	K562	blood:
10	chr15:44951575..44958275-chr15:45001046..45006983,19	MCF-7	breast:
11	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

No data

Variant related genes	Relation type
B2M	TF binding region
PATL2	TF binding region
ENSG00000206957	Chromatin interaction
ENSG00000127483	Chromatin interaction
ENSG00000229474	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000185880	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11853269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11856066	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12324005	1.00[ASW][hapmap]
rs13380093	1.00[ASW][hapmap]
rs16974273	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17235843	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235857	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17588305	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17589301	0.80[ASN][1000 genomes]
rs34569539	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3759880	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3759882	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759883	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759884	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161853	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs7164679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7167254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7175030	0.83[ASN][1000 genomes]
rs7182487	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45002000-45006000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr15:45002200-45006800	Active TSS	Colonic Mucosa	Colon
3	chr15:45002400-45006000	Active TSS	NHLF	lung
4	chr15:45002400-45006400	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr15:45002400-45006600	Active TSS	Lung	lung
6	chr15:45002400-45006600	Active TSS	Stomach Smooth Muscle	stomach
7	chr15:45002400-45006800	Active TSS	Small Intestine	intestine
8	chr15:45002400-45007000	Active TSS	Left Ventricle	heart
9	chr15:45002400-45007200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:45002400-45007200	Active TSS	Right Ventricle	heart
11	chr15:45002600-45006200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:45002600-45006200	Active TSS	Duodenum Mucosa	Duodenum
13	chr15:45002600-45006400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:45002600-45007200	Active TSS	Psoas Muscle	Psoas
15	chr15:45002800-45006000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:45002800-45006200	Active TSS	NHDF-Ad	bronchial
17	chr15:45002800-45006400	Active TSS	HSMMtube	muscle
18	chr15:45002800-45006600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:45002800-45006600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr15:45003000-45006000	Active TSS	Ovary	ovary
21	chr15:45003200-45011600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:45003400-45006600	Active TSS	Placenta	Placenta
23	chr15:45003800-45006600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
24	chr15:45003800-45006800	Transcr. at gene 5' and 3'	Dnd41	blood
25	chr15:45003800-45008200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
26	chr15:45003800-45010600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
27	chr15:45004000-45008400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:45004200-45006600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr15:45004200-45007800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
30	chr15:45004200-45012400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
31	chr15:45004400-45006000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:45004400-45006800	Active TSS	Right Atrium	heart
33	chr15:45004400-45008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:45004400-45009000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:45004400-45009400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
36	chr15:45004400-45009800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
37	chr15:45004600-45008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:45004800-45008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:45004800-45008800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:45005000-45006000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:45005000-45006000	Flanking Active TSS	HUVEC	blood vessel
43	chr15:45005000-45007200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr15:45005000-45007600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr15:45005000-45007600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:45005000-45018400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr15:45005000-45018600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:45005200-45006000	Flanking Active TSS	Osteobl	bone
49	chr15:45005200-45006200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:45005200-45006200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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