Variant report

Variant	rs16965748
Chromosome Location	chr17:38555557-38555558
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	CTCF	chr17:38555458-38555678	H1-hESC	embryonic stem cell:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
2	CTCF	chr17:38555440-38555590	A549	lung:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
3	CTCF	chr17:38555438-38555678	Medullo	brain:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
4	CTCF	chr17:38555480-38555630	GM12878	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
5	CTCF	chr17:38555480-38555667	GM10266	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
6	CTCF	chr17:38555480-38555630	HPF	lung:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
7	CTCF	chr17:38555480-38555750	GM12864	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
8	RAD21	chr17:38555422-38555728	GM12878	blood:	n/a	chr17:38555558-38555577
9	CTCF	chr17:38555480-38555630	HUVEC	blood vessel:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
10	CTCF	chr17:38555460-38555610	HEEpiC	esophagus:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
11	CTCF	chr17:38555420-38555570	HCPEpiC	choroid plexus:	n/a	n/a
12	RAD21	chr17:38555411-38555716	HepG2	liver:	n/a	chr17:38555558-38555577
13	CTCF	chr17:38555368-38555683	ECC-1	luminal epithelium:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
14	CTCF	chr17:38555460-38555610	HPAF	blood vessel:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
15	CTCF	chr17:38555433-38555775	MCF-7	breast:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
16	SMC3	chr17:38555386-38555731	Hela-S3	cervix:	n/a	chr17:38555559-38555573
17	CTCF	chr17:38555440-38555590	K562	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
18	CTCF	chr17:38555480-38555630	AoAF	blood vessel:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
19	CTCF	chr17:38555460-38555610	GM12873	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
20	POLR2A	chr17:38554779-38557569	K562	blood:	n/a	n/a
21	RAD21	chr17:38555135-38556138	SK-N-SH	brain:	n/a	chr17:38555558-38555577
22	RAD21	chr17:38555376-38555700	GM12878	blood:	n/a	chr17:38555558-38555577
23	RAD21	chr17:38555449-38555709	A549	lung:	n/a	chr17:38555558-38555577
24	CTCF	chr17:38555471-38555656	HepG2	liver:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
25	RAD21	chr17:38555423-38555775	SK-N-SH_RA	brain:	n/a	chr17:38555558-38555577
26	RAD21	chr17:38555267-38555848	HCT-116	colon:	n/a	chr17:38555558-38555577
27	CTCF	chr17:38555420-38555570	HRE	kidney:	n/a	n/a
28	CTCF	chr17:38555520-38555670	HepG2	liver:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
29	RAD21	chr17:38555344-38555802	H1-hESC	embryonic stem cell:	n/a	chr17:38555558-38555577
30	CTCF	chr17:38555460-38555610	HCPEpiC	choroid plexus:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
31	CTCF	chr17:38555480-38555630	AG04449	skin:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
32	CTCF	chr17:38555289-38555774	A549	lung:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
33	CTCF	chr17:38555332-38555755	HepG2	liver:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
34	CTCF	chr17:38555417-38555707	A549	lung:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
35	CTCF	chr17:38555480-38555630	SK-N-SH_RA	brain:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
36	CTCF	chr17:38555458-38555684	LNCaP	prostate:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
37	CTCF	chr17:38555440-38555590	Hela-S3	cervix:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
38	POLR2A	chr17:38555354-38556166	K562	blood:	n/a	n/a
39	CTCF	chr17:38555420-38555570	AoAF	blood vessel:	n/a	n/a
40	CTCF	chr17:38555176-38555930	HCT-116	colon:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
41	CTCF	chr17:38555432-38555717	H1-hESC	embryonic stem cell:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
42	RAD21	chr17:38555440-38555640	GM12878	blood:	n/a	chr17:38555558-38555577
43	RAD21	chr17:38555462-38555722	HepG2	liver:	n/a	chr17:38555558-38555577
44	CTCF	chr17:38555480-38555630	GM12873	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
45	CTCF	chr17:38555500-38555650	AG04449	skin:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
46	CTCF	chr17:38555460-38555610	GM12874	blood:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
47	CTCF	chr17:38555480-38555628	SK-N-SH_RA	brain:	n/a	chr17:38555559-38555580 chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
48	ARID3A	chr17:38555412-38555726	K562	blood:	n/a	n/a
49	CTCF	chr17:38555470-38555579	GM20000	blood:	n/a	chr17:38555558-38555574 chr17:38555557-38555575 chr17:38555560-38555573
50	CTCF	chr17:38555420-38555570	HMF	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38544588..38548116-chr17:38554882..38558246,4	K562	blood:
2	chr17:38544691..38546816-chr17:38554704..38556382,2	K562	blood:
3	chr17:38515380..38518267-chr17:38554821..38556502,2	K562	blood:
4	chr17:38555377..38556004-chr17:38599008..38599961,2	K562	blood:

Variant related genes	Relation type
TOP2A	TF binding region
ENSG00000222881	Chromatin interaction
ENSG00000266208	Chromatin interaction
ENSG00000131747	Chromatin interaction
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10451257	1.00[TSI][hapmap]
rs10512482	1.00[EUR][1000 genomes]
rs11540720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11867902	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12103533	1.00[EUR][1000 genomes]
rs15685	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs16965660	1.00[EUR][1000 genomes]
rs16965669	1.00[EUR][1000 genomes]
rs16965734	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965736	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965774	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965778	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616672	0.92[EUR][1000 genomes]
rs17616879	0.92[EUR][1000 genomes]
rs17617263	0.92[EUR][1000 genomes]
rs17678817	0.92[EUR][1000 genomes]
rs17678959	0.92[EUR][1000 genomes]
rs17678990	0.92[EUR][1000 genomes]
rs17679086	0.92[EUR][1000 genomes]
rs17679361	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17680217	0.92[EUR][1000 genomes]
rs17680410	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17680507	0.92[EUR][1000 genomes]
rs17680624	0.92[EUR][1000 genomes]
rs2012667	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2229773	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs28362320	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362321	0.92[EUR][1000 genomes]
rs33998939	0.92[EUR][1000 genomes]
rs34270904	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34300454	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35783632	0.92[EUR][1000 genomes]
rs35898909	0.92[EUR][1000 genomes]
rs41283417	1.00[EUR][1000 genomes]
rs41283423	0.92[EUR][1000 genomes]
rs4134993	0.92[EUR][1000 genomes]
rs4134998	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135005	0.92[EUR][1000 genomes]
rs4135007	0.92[EUR][1000 genomes]
rs4135012	0.92[EUR][1000 genomes]
rs4135019	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135021	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs4135027	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4135030	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs45612441	0.92[EUR][1000 genomes]
rs8067519	1.00[EUR][1000 genomes]
rs8071687	1.00[EUR][1000 genomes]
rs9889905	0.85[EUR][1000 genomes]
rs9891944	0.92[EUR][1000 genomes]
rs9894364	1.00[EUR][1000 genomes]
rs9894807	0.85[EUR][1000 genomes]
rs9895336	1.00[MEX][hapmap]
rs9898500	1.00[EUR][1000 genomes]
rs9903293	1.00[EUR][1000 genomes]
rs9909777	1.00[EUR][1000 genomes]
rs9909811	0.85[EUR][1000 genomes]
rs9910373	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38536800-38562000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr17:38537200-38558600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:38538200-38557400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:38538400-38559200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
6	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
7	chr17:38541800-38559000	Strong transcription	A549	lung
8	chr17:38542000-38556800	Weak transcription	Fetal Lung	lung
9	chr17:38542200-38571600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:38542400-38560400	Strong transcription	Dnd41	blood
11	chr17:38542600-38566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:38542600-38566400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:38542600-38571800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38543000-38557000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:38543000-38566000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr17:38543200-38559000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38543200-38571000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:38543400-38571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr17:38543400-38571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:38543400-38571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:38543800-38566000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:38543800-38566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr17:38543800-38566400	Weak transcription	Fetal Heart	heart
24	chr17:38544000-38561200	Strong transcription	Hela-S3	cervix
25	chr17:38544000-38566600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr17:38544000-38566800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr17:38544000-38569800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:38544000-38570200	Strong transcription	HepG2	liver
29	chr17:38544000-38571800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:38544200-38561400	Strong transcription	Osteobl	bone
31	chr17:38544200-38567000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:38544400-38566600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:38544400-38573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:38545200-38573200	Weak transcription	Gastric	stomach
35	chr17:38546000-38573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:38546400-38572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr17:38546400-38572800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:38546400-38573200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:38547800-38559000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:38547800-38565200	Weak transcription	Esophagus	oesophagus
41	chr17:38548200-38572000	Weak transcription	Brain Germinal Matrix	brain
42	chr17:38548400-38556800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr17:38548400-38572800	Weak transcription	Primary B cells from cord blood	blood
44	chr17:38549400-38557200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr17:38549800-38573000	Weak transcription	Fetal Intestine Large	intestine
46	chr17:38550400-38558000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:38551000-38573000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr17:38551600-38560600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:38552200-38564000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:38552200-38573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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