Variant report

Variant	rs62571021
Chromosome Location	chr9:15513536-15513537
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:131)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:131 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:15513520-15513670	K562	blood:	n/a	n/a
2	CTCF	chr9:15513480-15513630	GM12868	blood:	n/a	n/a
3	CTCF	chr9:15513511-15513718	GM19240	blood:	n/a	n/a
4	POLR2A	chr9:15513417-15513706	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr9:15513520-15513670	AoAF	blood vessel:	n/a	n/a
6	YY1	chr9:15513492-15513668	K562	blood:	n/a	n/a
7	CTCF	chr9:15513497-15513701	GM12891	blood:	n/a	n/a
8	CTCF	chr9:15513520-15513670	HA-sp	spinal cord:	n/a	n/a
9	CTCF	chr9:15513500-15513650	HEK293	kidney:	n/a	n/a
10	RAD21	chr9:15513420-15513696	GM12878	blood:	n/a	n/a
11	CTCF	chr9:15513504-15513704	MCF-7	breast:	n/a	n/a
12	CTCF	chr9:15513500-15513650	RPTEC	kidney:	n/a	n/a
13	CTCF	chr9:15513460-15513610	GM12873	blood:	n/a	n/a
14	CTCF	chr9:15513482-15513747	MCF-7	breast:	n/a	n/a
15	ZNF143	chr9:15513369-15513770	K562	blood:	n/a	n/a
16	MAZ	chr9:15512990-15513753	K562	blood:	n/a	n/a
17	RAD21	chr9:15513327-15513817	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr9:15512457-15513800	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr9:15513016-15513784	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr9:15513387-15513800	GM12878	blood:	n/a	n/a
21	EBF1	chr9:15513505-15513733	GM12878	blood:	n/a	n/a
22	RCOR1	chr9:15513398-15513719	K562	blood:	n/a	n/a
23	CTCF	chr9:15513500-15513650	GM12870	blood:	n/a	n/a
24	CTCF	chr9:15513500-15513650	GM12864	blood:	n/a	n/a
25	CTCF	chr9:15513500-15513650	GM12868	blood:	n/a	n/a
26	CTCF	chr9:15513440-15513590	AG09319	gingival:	n/a	n/a
27	CTCF	chr9:15513496-15513685	HepG2	liver:	n/a	n/a
28	CTCF	chr9:15513443-15513786	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr9:15513520-15513670	GM12866	blood:	n/a	n/a
30	CTCF	chr9:15513493-15513713	K562	blood:	n/a	n/a
31	JUND	chr9:15513416-15513724	K562	blood:	n/a	n/a
32	YY1	chr9:15513449-15513852	GM12878	blood:	n/a	n/a
33	CTCF	chr9:15513367-15513813	K562	blood:	n/a	n/a
34	POLR2A	chr9:15513338-15513659	GM12891	blood:	n/a	n/a
35	RAD21	chr9:15513439-15513728	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr9:15513339-15513881	MCF-7	breast:	n/a	n/a
37	CTCF	chr9:15513521-15513654	SK-N-SH_RA	brain:	n/a	n/a
38	HCFC1	chr9:15513393-15513683	K562	blood:	n/a	n/a
39	SMC3	chr9:15513451-15513779	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr9:15513091-15513785	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr9:15513500-15513650	MCF-7	breast:	n/a	n/a
42	CTCF	chr9:15513460-15513610	HFF-Myc	foreskin:	n/a	n/a
43	CTCF	chr9:15513500-15513650	GM12869	blood:	n/a	n/a
44	CTCF	chr9:15513500-15513650	NHDF-neo	bronchial:	n/a	n/a
45	CHD2	chr9:15512910-15513717	H1-hESC	embryonic stem cell:	n/a	n/a
46	KAP1	chr9:15513299-15513861	HEK293	kidney:	n/a	n/a
47	CTCF	chr9:15513500-15513650	HPAF	blood vessel:	n/a	n/a
48	CTCF	chr9:15513496-15513708	MCF-7	breast:	n/a	n/a
49	CTCF	chr9:15513507-15513717	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr9:15513381-15513869	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:15512114..15513693-chr9:15523609..15526046,2	MCF-7	breast:
2	chr9:15510264..15513012-chr9:15513420..15518300,5	K562	blood:
3	chr9:15511224..15513667-chr9:15516724..15518268,2	K562	blood:
4	chr9:15510312..15513012-chr9:15513420..15514921,2	K562	blood:

No data

Variant related genes	Relation type
PSIP1	TF binding region
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12682808	0.90[ASN][1000 genomes]
rs16933316	0.92[ASN][1000 genomes]
rs16933350	0.80[EUR][1000 genomes]
rs1828382	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56361298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57142629	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57191285	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57467578	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57849124	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58915725	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59520337	0.80[EUR][1000 genomes]
rs62571018	0.80[EUR][1000 genomes]
rs62571022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62571029	0.80[EUR][1000 genomes]
rs62571031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62571032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7023730	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73408328	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73408340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73410253	0.89[ASN][1000 genomes]
rs73410254	0.89[ASN][1000 genomes]
rs73644655	0.97[ASN][1000 genomes]
rs7856710	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7857933	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7862428	0.85[ASN][1000 genomes]
rs7863139	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62571021	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15511400-15513600	Flanking Active TSS	GM12878-XiMat	blood
2	chr9:15511800-15513600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr9:15511800-15513600	Enhancers	Primary T cells from cord blood	blood
4	chr9:15511800-15513600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:15511800-15513600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr9:15511800-15513800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr9:15511800-15513800	Enhancers	Primary B cells from cord blood	blood
8	chr9:15511800-15513800	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:15511800-15513800	Enhancers	Primary hematopoietic stem cells	blood
10	chr9:15511800-15513800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr9:15511800-15513800	Enhancers	Fetal Thymus	thymus
12	chr9:15512400-15515000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:15512600-15513600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:15512600-15513600	Weak transcription	Thymus	Thymus
15	chr9:15512600-15514200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:15512800-15513800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:15513200-15513600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:15513200-15513600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
19	chr9:15513200-15513600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr9:15513200-15513600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr9:15513200-15513600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr9:15513200-15513600	Flanking Active TSS	K562	blood
23	chr9:15513200-15513800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr9:15513200-15513800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr9:15513200-15513800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr9:15513400-15513600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:15513400-15513600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr9:15513400-15513600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:15513400-15513600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:15513400-15513600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:15513400-15513600	Enhancers	A549	lung
32	chr9:15513400-15513800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr9:15513400-15514400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr9:15513400-15521800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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