Variant report

Variant	rs17828907
Chromosome Location	chr14:69011205-69011206
allele	A/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	FOXM1	chr14:69010956-69012525	ECC-1	luminal epithelium:	n/a	n/a
2	FOS	chr14:69010793-69011460	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr14:69010859-69011464	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr14:69010796-69011714	IMR90	lung:	n/a	n/a
5	FOS	chr14:69010798-69011487	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr14:69010765-69011389	MCF10A-Er-Src	breast:	n/a	n/a
7	EGR1	chr14:69010639-69011456	HCT-116	colon:	n/a	chr14:69010971-69010984 chr14:69010972-69010983 chr14:69010970-69010984 chr14:69010971-69010984 chr14:69010972-69010982 chr14:69010972-69010983 chr14:69010972-69010982 chr14:69010966-69010988
8	STAT3	chr14:69010870-69011425	MCF10A-Er-Src	breast:	n/a	n/a
9	NFIC	chr14:69010408-69011447	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr14:69010283-69012485	MCF10A-Er-Src	breast:	n/a	n/a
11	PBX3	chr14:69010525-69011299	SK-N-SH	brain:	n/a	n/a
12	NFIC	chr14:69010965-69011871	ECC-1	luminal epithelium:	n/a	chr14:69011438-69011454
13	EGR1	chr14:69010686-69011302	HCT-116	colon:	n/a	chr14:69010971-69010984 chr14:69010972-69010983 chr14:69010970-69010984 chr14:69010971-69010984 chr14:69010972-69010982 chr14:69010972-69010983 chr14:69010972-69010982 chr14:69010966-69010988
14	POLR2A	chr14:69010249-69011449	U87	brain:	n/a	n/a
15	RFX5	chr14:69010453-69011456	SK-N-SH	brain:	n/a	n/a
16	TCF12	chr14:69010976-69012489	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr14:69010757-69012531	ECC-1	luminal epithelium:	n/a	chr14:69012108-69012122
18	CEBPB	chr14:69010894-69011277	IMR90	lung:	n/a	n/a
19	FOS	chr14:69010802-69011457	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr14:69010756-69011289	SK-N-SH_RA	brain:	n/a	n/a
21	MYC	chr14:69010741-69011575	MCF10A-Er-Src	breast:	n/a	chr14:69011381-69011392
22	FOSL2	chr14:69010763-69011306	SK-N-SH	brain:	n/a	n/a
23	EP300	chr14:69011090-69011927	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr14:69010385-69011863	U87	brain:	n/a	n/a
25	TEAD4	chr14:69011111-69011969	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr14:69010334-69011863	U87	brain:	n/a	n/a
27	E2F4	chr14:69010891-69011336	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr14:69010904-69011396	MCF10A-Er-Src	breast:	n/a	n/a
29	NFIC	chr14:69010846-69012388	ECC-1	luminal epithelium:	n/a	chr14:69011438-69011454
30	POLR2A	chr14:69010843-69011680	IMR90	lung:	n/a	n/a
31	FOS	chr14:69010836-69011334	HUVEC	blood vessel:	n/a	n/a
32	MAFK	chr14:69010899-69011349	IMR90	lung:	n/a	n/a
33	POLR2A	chr14:69010545-69011472	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr14:69010851-69011515	MCF10A-Er-Src	breast:	n/a	chr14:69011381-69011392
35	FOS	chr14:69010848-69011427	MCF10A-Er-Src	breast:	n/a	n/a
36	RAD21	chr14:69010800-69011292	IMR90	lung:	n/a	n/a
37	GATA3	chr14:69010440-69011348	SK-N-SH	brain:	n/a	chr14:69011224-69011232

Variant related genes	Relation type
RAD51B	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10483812	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10483813	0.85[CEU][hapmap];0.91[AMR][1000 genomes]
rs11621276	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11624097	0.85[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11624164	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11624333	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11628293	0.84[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11844632	0.92[ASN][1000 genomes]
rs12889251	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17105780	0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17105847	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17755734	1.00[MKK][hapmap]
rs17755752	1.00[MKK][hapmap]
rs17755925	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17756000	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17756147	0.91[AMR][1000 genomes]
rs17828955	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158357	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34636650	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34882439	0.92[ASN][1000 genomes]
rs36028293	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71423314	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71423316	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71423317	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71423318	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739874	0.85[AMR][1000 genomes]
rs999737	0.85[CEU][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes]

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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv516239	chr14:69010690-69025870	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69002400-69016600	Weak transcription	Gastric	stomach
2	chr14:69005000-69013400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:69005000-69015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:69006000-69014600	Enhancers	NHDF-Ad	bronchial
5	chr14:69006200-69012000	Weak transcription	Lung	lung
6	chr14:69006400-69013200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr14:69006400-69013800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:69006800-69011600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr14:69006800-69012800	Weak transcription	Esophagus	oesophagus
10	chr14:69006800-69013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:69006800-69014200	Weak transcription	Brain Substantia Nigra	brain
12	chr14:69006800-69014400	Weak transcription	Brain Hippocampus Middle	brain
13	chr14:69006800-69014600	Weak transcription	Brain Angular Gyrus	brain
14	chr14:69007000-69011400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr14:69007200-69013400	Weak transcription	Right Ventricle	heart
16	chr14:69007400-69013600	Weak transcription	Fetal Heart	heart
17	chr14:69007800-69013800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:69007800-69014000	Weak transcription	Brain Anterior Caudate	brain
19	chr14:69008000-69013800	Enhancers	HMEC	breast
20	chr14:69008000-69013800	Enhancers	HSMM	muscle
21	chr14:69008200-69013400	Weak transcription	Ovary	ovary
22	chr14:69008400-69011600	Weak transcription	Fetal Intestine Small	intestine
23	chr14:69008400-69011800	Weak transcription	Spleen	Spleen
24	chr14:69008400-69013600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:69008400-69013600	Weak transcription	Fetal Kidney	kidney
26	chr14:69008400-69013800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:69008400-69014200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:69009000-69012200	Enhancers	Osteobl	bone
29	chr14:69009000-69013400	Enhancers	NHEK	skin
30	chr14:69009000-69013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr14:69009000-69023600	Enhancers	Fetal Muscle Leg	muscle
32	chr14:69009200-69012200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr14:69009200-69013400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr14:69009200-69016600	Enhancers	Colon Smooth Muscle	Colon
35	chr14:69009400-69013400	Enhancers	Rectal Smooth Muscle	rectum
36	chr14:69009400-69017600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:69009600-69014600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:69009600-69016000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr14:69009800-69012400	Enhancers	Psoas Muscle	Psoas
40	chr14:69009800-69012400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr14:69009800-69013800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:69010000-69011800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr14:69010000-69013600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr14:69010200-69012000	Enhancers	Fetal Lung	lung
45	chr14:69010200-69012200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr14:69010200-69013400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:69010400-69011400	Enhancers	Adipose Nuclei	Adipose
48	chr14:69010400-69011400	Enhancers	Stomach Smooth Muscle	stomach
49	chr14:69010400-69012000	Enhancers	Right Atrium	heart
50	chr14:69010400-69012200	Enhancers	HSMMtube	muscle

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