Variant report

Variant	rs16956602
Chromosome Location	chr15:72448111-72448112
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	TCF12	chr15:72447141-72448639	ECC-1	luminal epithelium:	n/a	chr15:72447543-72447553 chr15:72447833-72447840
2	RAD21	chr15:72447870-72448954	MCF-7	breast:	n/a	chr15:72448539-72448558
3	RAD21	chr15:72448083-72448894	MCF-7	breast:	n/a	chr15:72448539-72448558
4	CHD1	chr15:72447635-72448867	IMR90	lung:	n/a	n/a
5	SMC3	chr15:72447140-72448918	SK-N-SH	brain:	n/a	chr15:72448543-72448557
6	TCF12	chr15:72447156-72448931	A549	lung:	n/a	chr15:72447543-72447553 chr15:72447833-72447840
7	RAD21	chr15:72448108-72448736	A549	lung:	n/a	chr15:72448539-72448558
8	TCF12	chr15:72447100-72448524	ECC-1	luminal epithelium:	n/a	chr15:72447543-72447553 chr15:72447833-72447840
9	NFIC	chr15:72446994-72448594	ECC-1	luminal epithelium:	n/a	chr15:72447488-72447504 chr15:72447723-72447739
10	CTCF	chr15:72448060-72448210	HEK293	kidney:	n/a	n/a
11	RAD21	chr15:72448060-72448779	H1-hESC	embryonic stem cell:	n/a	chr15:72448539-72448558
12	MAX	chr15:72447553-72448167	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr15:72448100-72448250	AG04450	lung:	n/a	n/a
14	MAX	chr15:72447088-72448645	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr15:72447091-72448744	ECC-1	luminal epithelium:	n/a	chr15:72447488-72447504 chr15:72447723-72447739
16	ZNF263	chr15:72447523-72448903	HEK293-T-REx	kidney:	n/a	n/a
17	RAD21	chr15:72448090-72448780	H1-hESC	embryonic stem cell:	n/a	chr15:72448539-72448558
18	RAD21	chr15:72448098-72448820	A549	lung:	n/a	chr15:72448539-72448558
19	MAX	chr15:72447500-72448131	A549	lung:	n/a	n/a
20	SPI1	chr15:72448016-72448740	GM12878	blood:	n/a	n/a
21	E2F6	chr15:72447393-72448686	A549	lung:	n/a	n/a
22	FOXA2	chr15:72447393-72448113	A549	lung:	n/a	n/a
23	MAX	chr15:72447545-72448135	MCF-7	breast:	n/a	n/a
24	TEAD4	chr15:72447161-72448341	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr15:72447002-72448288	ECC-1	luminal epithelium:	n/a	n/a
26	TEAD4	chr15:72447082-72448145	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr15:72446967-72449247	A549	lung:	n/a	chr15:72448543-72448556 chr15:72448541-72448559
28	POLR2A	chr15:72447284-72448407	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr15:72448024-72449011	A549	lung:	n/a	chr15:72448539-72448558
30	MAX	chr15:72447238-72448205	ECC-1	luminal epithelium:	n/a	n/a
31	RAD21	chr15:72447214-72448947	ECC-1	luminal epithelium:	n/a	chr15:72447815-72447828 chr15:72448539-72448558
32	NFIC	chr15:72447418-72448122	SK-N-SH	brain:	n/a	chr15:72447488-72447504 chr15:72447723-72447739
33	RAD21	chr15:72448076-72448811	ECC-1	luminal epithelium:	n/a	chr15:72448539-72448558
34	MAX	chr15:72447306-72448858	A549	lung:	n/a	n/a
35	RAD21	chr15:72447946-72448766	IMR90	lung:	n/a	chr15:72448539-72448558
36	MAX	chr15:72447431-72448142	MCF-7	breast:	n/a	n/a
37	ELF1	chr15:72448110-72448667	GM12878	blood:	n/a	n/a
38	ELF1	chr15:72447445-72448866	MCF-7	breast:	n/a	n/a
39	RAD21	chr15:72447315-72449103	SK-N-SH	brain:	n/a	chr15:72447815-72447828 chr15:72448539-72448558
40	RAD21	chr15:72448063-72448971	HCT-116	colon:	n/a	chr15:72448539-72448558
41	SMC3	chr15:72448110-72448745	GM12878	blood:	n/a	chr15:72448543-72448557
42	FOSL2	chr15:72447433-72448804	A549	lung:	n/a	chr15:72448568-72448577
43	CTCF	chr15:72447980-72448130	A549	lung:	n/a	n/a
44	CTCF	chr15:72447438-72448994	SK-N-SH	brain:	n/a	chr15:72448543-72448556 chr15:72448541-72448559
45	RAD21	chr15:72448037-72448794	SK-N-SH_RA	brain:	n/a	chr15:72448539-72448558
46	SPI1	chr15:72448107-72448728	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:72093395..72094147-chr15:72448020..72448826,2	K562	blood:
2	chr15:72095167..72095784-chr15:72448077..72448830,3	MCF-7	breast:
3	chr15:72076704..72077706-chr15:72447990..72448967,6	K562	blood:
4	chr15:72445875..72448342-chr15:72461656..72463455,2	MCF-7	breast:
5	chr15:72045149..72045729-chr15:72448063..72448589,2	K562	blood:
6	chr15:72094781..72095719-chr15:72448020..72449479,6	K562	blood:
7	chr15:72045078..72045591-chr15:72448055..72448912,2	MCF-7	breast:
8	chr15:72094281..72095669-chr15:72448048..72449003,4	MCF-7	breast:
9	chr15:72035950..72036579-chr15:72447850..72448622,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260173	TF binding region
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11072341	0.90[ASN][1000 genomes]
rs11072343	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072344	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072355	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs1120002	0.90[ASN][1000 genomes]
rs12437582	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12438532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439689	0.94[ASN][1000 genomes]
rs12440204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12440299	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440435	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs12440927	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12441246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441470	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441567	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12441622	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442680	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443127	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592615	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592858	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592932	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592969	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593857	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593946	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594297	0.90[EUR][1000 genomes]
rs12911449	1.00[CEU][hapmap]
rs1426168	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1545825	0.86[ASN][1000 genomes]
rs16953770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16956539	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16956599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16956723	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs1871834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs2288256	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2305705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28397923	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28639924	0.90[ASN][1000 genomes]
rs28653163	0.90[ASN][1000 genomes]
rs28701834	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912226	1.00[CEU][hapmap]
rs2912229	1.00[CEU][hapmap]
rs2929514	0.80[ASN][1000 genomes]
rs2929515	0.80[ASN][1000 genomes]
rs2929521	0.86[ASN][1000 genomes]
rs2929522	0.86[ASN][1000 genomes]
rs2929524	0.80[ASN][1000 genomes]
rs2929530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs2929531	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2929533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2957369	0.86[ASN][1000 genomes]
rs2957729	0.80[ASN][1000 genomes]
rs2957730	0.80[ASN][1000 genomes]
rs2957741	0.86[ASN][1000 genomes]
rs2957747	0.86[ASN][1000 genomes]
rs2957749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs2959915	1.00[CEU][hapmap]
rs34625473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35773391	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3803388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3809505	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825869	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4442765	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4511484	0.86[ASN][1000 genomes]
rs6495000	1.00[CEU][hapmap]
rs7161909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7164646	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7165735	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7171446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8026894	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs8039245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8192381	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9920148	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72446400-72448200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:72447200-72448800	Flanking Active TSS	A549	lung
3	chr15:72447400-72448200	Active TSS	Pancreas	Pancrea
4	chr15:72447400-72448600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:72447400-72448600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr15:72447400-72448600	Flanking Active TSS	Liver	Liver
7	chr15:72447400-72448600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr15:72447400-72448600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr15:72447400-72448800	Flanking Active TSS	HMEC	breast
10	chr15:72447400-72449000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:72447400-72449000	Active TSS	Colonic Mucosa	Colon
12	chr15:72447400-72449000	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr15:72447400-72449200	Active TSS	Fetal Kidney	kidney
14	chr15:72447600-72448200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
15	chr15:72447600-72448200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr15:72447600-72448200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:72447600-72448200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr15:72447600-72448200	Enhancers	Fetal Heart	heart
19	chr15:72447600-72448200	Flanking Active TSS	Fetal Intestine Small	intestine
20	chr15:72447600-72448200	Flanking Active TSS	Fetal Stomach	stomach
21	chr15:72447600-72448200	Flanking Active TSS	Osteobl	bone
22	chr15:72447600-72448400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:72447600-72448400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:72447600-72448400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:72447600-72448400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:72447600-72448400	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr15:72447600-72448400	Flanking Active TSS	HSMMtube	muscle
28	chr15:72447600-72448400	Flanking Active TSS	NH-A	brain
29	chr15:72447600-72448600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:72447600-72448600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr15:72447600-72448600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:72447600-72448600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr15:72447600-72448600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr15:72447600-72448600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr15:72447600-72448600	Active TSS	Colon Smooth Muscle	Colon
36	chr15:72447600-72448600	Active TSS	Fetal Brain Female	brain
37	chr15:72447600-72448600	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr15:72447600-72448600	Active TSS	Gastric	stomach
39	chr15:72447600-72448600	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr15:72447600-72448600	Active TSS	Right Atrium	heart
41	chr15:72447600-72448600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr15:72447600-72448600	Active TSS	NHDF-Ad	bronchial
43	chr15:72447600-72448600	Flanking Active TSS	NHEK	skin
44	chr15:72447600-72448800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:72447600-72448800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:72447600-72448800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:72447600-72448800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:72447600-72449000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr15:72447800-72448200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:72447800-72448200	Enhancers	Primary T helper cells fromperipheralblood	blood

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