Variant report

Variant	rs16973883
Chromosome Location	chr17:67265361-67265362
allele	G/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	EP300	chr17:67264812-67265655	HepG2	liver:	n/a	chr17:67265128-67265142 chr17:67265479-67265493
2	CEBPB	chr17:67264657-67265756	HepG2	liver:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265044-67265057 chr17:67265481-67265494 chr17:67265481-67265492
3	GATA3	chr17:67265194-67266235	A549	lung:	n/a	n/a
4	STAT3	chr17:67264889-67266372	MCF10A-Er-Src	breast:	n/a	chr17:67265307-67265315
5	JUND	chr17:67265348-67266151	SK-N-SH	brain:	n/a	n/a
6	SIN3AK20	chr17:67265271-67266196	MCF-7	breast:	n/a	n/a
7	MAFK	chr17:67265352-67266008	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr17:67264698-67265934	HepG2	liver:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265044-67265057 chr17:67265481-67265494 chr17:67265481-67265492
9	EP300	chr17:67265284-67266241	SK-N-SH	brain:	n/a	chr17:67265479-67265493
10	EP300	chr17:67265269-67266323	SK-N-SH	brain:	n/a	chr17:67266256-67266270 chr17:67265479-67265493
11	FOSL2	chr17:67265353-67266331	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr17:67265183-67266363	SK-N-SH	brain:	n/a	n/a
13	BRCA1	chr17:67265205-67265899	Hela-S3	cervix:	n/a	n/a
14	RFX5	chr17:67264717-67265402	HepG2	liver:	n/a	n/a
15	TCF12	chr17:67265301-67266208	SK-N-SH	brain:	n/a	n/a
16	STAT3	chr17:67264907-67266176	MCF10A-Er-Src	breast:	n/a	chr17:67265307-67265315
17	NFIC	chr17:67265304-67266203	SK-N-SH	brain:	n/a	n/a
18	FOS	chr17:67265132-67266013	MCF10A-Er-Src	breast:	n/a	n/a
19	CEBPB	chr17:67265197-67265874	MCF-7	breast:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265481-67265494 chr17:67265481-67265492
20	CEBPB	chr17:67264817-67265997	A549	lung:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265044-67265057 chr17:67265481-67265494 chr17:67265481-67265492
21	JUND	chr17:67265177-67265964	Hela-S3	cervix:	n/a	n/a
22	STAT3	chr17:67264903-67266201	MCF10A-Er-Src	breast:	n/a	chr17:67265307-67265315
23	JUND	chr17:67264701-67265890	HepG2	liver:	n/a	n/a
24	FOS	chr17:67264908-67266243	MCF10A-Er-Src	breast:	n/a	n/a
25	TEAD4	chr17:67264624-67266072	HepG2	liver:	n/a	n/a
26	RFX5	chr17:67264753-67266140	Hela-S3	cervix:	n/a	n/a
27	FOXA1	chr17:67264556-67265674	HepG2	liver:	n/a	chr17:67265474-67265486
28	ZNF217	chr17:67265245-67265905	MCF-7	breast:	n/a	n/a
29	POLR2A	chr17:67265352-67265892	MCF10A-Er-Src	breast:	n/a	n/a
30	RCOR1	chr17:67264726-67265574	HepG2	liver:	n/a	n/a
31	ARID3A	chr17:67264482-67266037	HepG2	liver:	n/a	n/a
32	SP1	chr17:67265261-67266094	A549	lung:	n/a	n/a
33	FOXA2	chr17:67265278-67265643	HepG2	liver:	n/a	chr17:67265474-67265486
34	CEBPB	chr17:67264750-67266177	Hela-S3	cervix:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265044-67265057 chr17:67265481-67265494 chr17:67265481-67265492
35	EP300	chr17:67264910-67266099	Hela-S3	cervix:	n/a	chr17:67265128-67265142 chr17:67265479-67265493
36	E2F4	chr17:67264951-67265844	MCF10A-Er-Src	breast:	n/a	n/a
37	TCF12	chr17:67265248-67266381	SK-N-SH	brain:	n/a	n/a
38	TEAD4	chr17:67265290-67266224	SK-N-SH	brain:	n/a	n/a
39	FOS	chr17:67265008-67266231	MCF10A-Er-Src	breast:	n/a	n/a
40	CEBPB	chr17:67265288-67265706	K562	blood:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265481-67265494 chr17:67265481-67265492
41	POLR2A	chr17:67265129-67265647	MCF10A-Er-Src	breast:	n/a	n/a
42	BCL3	chr17:67265338-67265896	A549	lung:	n/a	n/a
43	MEF2A	chr17:67265343-67266144	SK-N-SH	brain:	n/a	n/a
44	GATA3	chr17:67265099-67265988	MCF-7	breast:	n/a	n/a
45	GATA3	chr17:67265262-67266375	SK-N-SH	brain:	n/a	n/a
46	CEBPB	chr17:67265155-67265890	IMR90	lung:	n/a	chr17:67265481-67265494 chr17:67265546-67265559 chr17:67265481-67265494 chr17:67265481-67265492
47	TCF7L2	chr17:67265004-67266019	HepG2	liver:	n/a	chr17:67265915-67265929
48	EP300	chr17:67265304-67265686	HepG2	liver:	n/a	chr17:67265479-67265493
49	MEF2A	chr17:67265246-67266252	SK-N-SH	brain:	n/a	n/a
50	TCF7L2	chr17:67265235-67266089	Hela-S3	cervix:	n/a	chr17:67265915-67265929

Variant related genes	Relation type
ABCA5	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1476749	0.87[ASW][hapmap];0.81[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973905	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17776943	1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes]
rs2067851	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496489	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28592152	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4553686	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4968854	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58324131	1.00[AMR][1000 genomes]
rs60350983	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208451	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225918	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73998226	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9302899	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9889277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894965	0.94[ASN][1000 genomes]
rs9895649	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs9908248	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9910364	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912665	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv1055156	chr17:67239695-67272311	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a
5	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
7	nsv457890	chr17:67264339-67327806	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a
8	nsv575936	chr17:67264339-67327806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16973883	ABCA10	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
2	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:67236000-67283000	Weak transcription	Ovary	ovary
4	chr17:67236400-67278000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:67236800-67280800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
7	chr17:67238800-67278000	Weak transcription	Thymus	Thymus
8	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
9	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
13	chr17:67245800-67278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:67248000-67284400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:67249000-67278400	Weak transcription	Fetal Intestine Small	intestine
16	chr17:67250000-67289200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:67250200-67280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:67250800-67277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:67251200-67279000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:67251400-67272000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:67251400-67273000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr17:67251400-67277600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:67251400-67277800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr17:67251400-67278000	Weak transcription	Primary T cells from cord blood	blood
25	chr17:67251600-67265800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr17:67251600-67265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr17:67251600-67274000	Weak transcription	GM12878-XiMat	blood
28	chr17:67251600-67278200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr17:67251600-67289200	Weak transcription	Brain Anterior Caudate	brain
30	chr17:67252400-67272400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:67253200-67278200	Weak transcription	Placenta	Placenta
32	chr17:67255600-67272000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr17:67257600-67278000	Weak transcription	Adipose Nuclei	Adipose
34	chr17:67259800-67271800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr17:67261000-67273000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:67261200-67265400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:67261400-67279200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:67261400-67322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr17:67264000-67265400	Enhancers	HUVEC	blood vessel
40	chr17:67264400-67265400	Flanking Active TSS	HepG2	liver
41	chr17:67264400-67266000	Flanking Active TSS	A549	lung
42	chr17:67264400-67268400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr17:67264600-67265400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr17:67264600-67265800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:67264600-67266200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:67264600-67266200	Enhancers	Osteobl	bone
47	chr17:67264800-67265400	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr17:67264800-67265800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:67264800-67266000	Enhancers	HMEC	breast
50	chr17:67264800-67266200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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