Variant report

Variant	rs16960545
Chromosome Location	chr17:19837012-19837013
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	RFX5	chr17:19836628-19837325	SK-N-SH	brain:	n/a	n/a
2	RFX5	chr17:19836951-19837235	HepG2	liver:	n/a	n/a
3	RFX5	chr17:19836933-19837314	Hela-S3	cervix:	n/a	n/a
4	NFYB	chr17:19836948-19837212	Hela-S3	cervix:	n/a	n/a
5	RFX5	chr17:19836680-19837271	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19836067..19837621-chr17:19839405..19840944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266126	TF binding region
AKAP10	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs16960602	1.00[EUR][1000 genomes]
rs281366	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs281367	1.00[ASN][1000 genomes]
rs28424266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28581607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28653561	1.00[EUR][1000 genomes]
rs28767032	1.00[EUR][1000 genomes]
rs28865331	1.00[EUR][1000 genomes]
rs6587207	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs6587211	1.00[ASN][1000 genomes]
rs7207459	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs7215639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215769	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219487	1.00[ASN][1000 genomes]
rs7224419	1.00[EUR][1000 genomes]
rs7224567	1.00[EUR][1000 genomes]
rs7224713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224875	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs8065122	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8068015	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068488	1.00[EUR][1000 genomes]
rs8071670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079093	1.00[EUR][1000 genomes]
rs8079487	1.00[EUR][1000 genomes]
rs8080190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs9889938	1.00[EUR][1000 genomes]
rs9890105	1.00[ASN][1000 genomes]
rs9892271	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9893296	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9894666	1.00[EUR][1000 genomes]
rs9895556	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9896499	1.00[EUR][1000 genomes]
rs9896633	1.00[EUR][1000 genomes]
rs9896641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897430	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898618	1.00[EUR][1000 genomes]
rs9900510	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9902663	1.00[EUR][1000 genomes]
rs9903631	1.00[EUR][1000 genomes]
rs9904059	1.00[EUR][1000 genomes]
rs9908415	1.00[EUR][1000 genomes]
rs9911408	1.00[EUR][1000 genomes]
rs9911872	1.00[EUR][1000 genomes]
rs9912184	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912648	1.00[EUR][1000 genomes]
rs9913858	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914502	1.00[ASN][1000 genomes]
rs9915039	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs9915413	1.00[EUR][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	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19802800-19844400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:19802800-19846400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:19802800-19852400	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr17:19803000-19851800	Strong transcription	Fetal Thymus	thymus
5	chr17:19803200-19840800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19803600-19845400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:19803600-19848000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:19804000-19844400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr17:19804000-19853000	Strong transcription	Dnd41	blood
10	chr17:19806200-19844000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:19806200-19844600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr17:19806400-19846200	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr17:19807800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:19809400-19837400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:19812200-19845400	Strong transcription	Liver	Liver
16	chr17:19815000-19838600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:19816800-19844400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:19817800-19844200	Weak transcription	Stomach Mucosa	stomach
19	chr17:19818600-19839400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:19819600-19844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:19821000-19838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:19821000-19842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:19823400-19837600	Weak transcription	Psoas Muscle	Psoas
24	chr17:19824400-19840200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:19824800-19840400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:19824800-19844200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:19824800-19845800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:19825000-19843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:19825000-19845200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:19825200-19848400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr17:19825200-19851800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:19826400-19840400	Strong transcription	Fetal Lung	lung
33	chr17:19826600-19840800	Strong transcription	Primary B cells from cord blood	blood
34	chr17:19827600-19851600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:19827600-19852800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr17:19828200-19837800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:19828400-19838000	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:19828400-19838400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr17:19828800-19839400	Weak transcription	K562	blood
40	chr17:19830000-19842800	Strong transcription	Fetal Intestine Small	intestine
41	chr17:19830000-19843200	Strong transcription	Fetal Stomach	stomach
42	chr17:19830000-19843400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:19830200-19839000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:19830200-19840400	Strong transcription	Fetal Intestine Large	intestine
45	chr17:19830600-19851200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:19831600-19840800	Strong transcription	Adipose Nuclei	Adipose
47	chr17:19831600-19841200	Strong transcription	GM12878-XiMat	blood
48	chr17:19831600-19843400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:19831600-19851400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr17:19831800-19843800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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