Variant report

Variant	rs62439722
Chromosome Location	chr7:6764940-6764941
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	MTA3	chr7:6764549-6765151	GM12878	blood:	n/a	n/a
2	WRNIP1	chr7:6764754-6764958	GM12878	blood:	n/a	n/a
3	MYC	chr7:6764742-6764962	NB4	blood:	n/a	n/a
4	MEF2A	chr7:6764651-6765115	GM12878	blood:	n/a	chr7:6764891-6764899
5	EP300	chr7:6764661-6765013	GM12878	blood:	n/a	n/a
6	SPI1	chr7:6764530-6765000	GM12891	blood:	n/a	chr7:6764852-6764865 chr7:6764737-6764744 chr7:6764851-6764864 chr7:6764853-6764862
7	TBP	chr7:6764715-6765065	GM12878	blood:	n/a	n/a
8	RCOR1	chr7:6764687-6764991	GM12878	blood:	n/a	n/a
9	POU2F2	chr7:6764452-6764995	GM12878	blood:	n/a	n/a
10	MAX	chr7:6764670-6764965	NB4	blood:	n/a	n/a
11	STAT5A	chr7:6764640-6765102	GM12878	blood:	n/a	n/a
12	RXRA	chr7:6764568-6764941	GM12878	blood:	n/a	n/a
13	EBF1	chr7:6764638-6764963	GM12878	blood:	n/a	n/a
14	IKZF1	chr7:6764610-6765107	GM12878	blood:	n/a	n/a
15	BHLHE40	chr7:6764639-6765044	GM12878	blood:	n/a	n/a
16	TCF12	chr7:6764538-6765000	GM12878	blood:	n/a	n/a
17	BCL11A	chr7:6764490-6765004	GM12878	blood:	n/a	n/a
18	RELA	chr7:6764709-6765249	GM19099	blood:	n/a	n/a
19	MAX	chr7:6764687-6765110	GM12878	blood:	n/a	n/a
20	SPI1	chr7:6764624-6765009	HL-60	blood:	n/a	chr7:6764852-6764865 chr7:6764737-6764744 chr7:6764851-6764864 chr7:6764853-6764862
21	TBL1XR1	chr7:6764670-6765080	GM12878	blood:	n/a	n/a
22	BATF	chr7:6764386-6765017	GM12878	blood:	n/a	n/a
23	ATF2	chr7:6764660-6765106	GM12878	blood:	n/a	n/a
24	SMC3	chr7:6764764-6764964	GM12878	blood:	n/a	n/a
25	PAX5	chr7:6764487-6764959	GM12878	blood:	n/a	n/a
26	FOXM1	chr7:6764580-6765181	GM12878	blood:	n/a	n/a
27	ZNF384	chr7:6764704-6765961	GM12878	blood:	n/a	n/a
28	EP300	chr7:6764721-6764986	GM12878	blood:	n/a	n/a
29	SP1	chr7:6764550-6765079	GM12878	blood:	n/a	chr7:6764943-6764950
30	BCLAF1	chr7:6764543-6765036	GM12878	blood:	n/a	n/a
31	TCF3	chr7:6764490-6764970	GM12878	blood:	n/a	n/a
32	PML	chr7:6764511-6765112	GM12878	blood:	n/a	n/a
33	NFIC	chr7:6764529-6765121	GM12878	blood:	n/a	n/a
34	SPI1	chr7:6764530-6765017	GM12878	blood:	n/a	chr7:6764852-6764865 chr7:6764737-6764744 chr7:6764851-6764864 chr7:6764853-6764862
35	BCL3	chr7:6764602-6765093	GM12878	blood:	n/a	n/a
36	RUNX3	chr7:6764553-6765169	GM12878	blood:	n/a	chr7:6764801-6764818
37	CHD1	chr7:6764785-6765290	GM12878	blood:	n/a	n/a
38	RUNX3	chr7:6764549-6765172	GM12878	blood:	n/a	chr7:6764801-6764818
39	IRF4	chr7:6764428-6765001	GM12878	blood:	n/a	n/a
40	RELA	chr7:6764641-6765253	GM18951	blood:	n/a	n/a
41	NFIC	chr7:6764565-6765204	GM12878	blood:	n/a	n/a
42	SPI1	chr7:6764499-6765142	GM12878	blood:	n/a	chr7:6764852-6764865 chr7:6764737-6764744 chr7:6764851-6764864 chr7:6764853-6764862
43	PAX5	chr7:6764326-6765121	GM12878	blood:	n/a	n/a
44	MXI1	chr7:6764675-6765004	GM12878	blood:	n/a	n/a
45	IRF4	chr7:6764446-6764973	GM12878	blood:	n/a	n/a
46	ATF2	chr7:6764577-6765116	GM12878	blood:	n/a	n/a
47	SP1	chr7:6764537-6765102	GM12878	blood:	n/a	chr7:6764943-6764950
48	STAT5A	chr7:6764640-6765032	GM12878	blood:	n/a	n/a
49	FOXM1	chr7:6764437-6765166	GM12878	blood:	n/a	n/a
50	MAZ	chr7:6764754-6764987	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PMS2CL	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10272921	0.82[ASN][1000 genomes]
rs12113879	0.92[ASN][1000 genomes]
rs12533770	0.88[AMR][1000 genomes]
rs12534591	0.80[ASN][1000 genomes]
rs12535850	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12536067	0.91[AMR][1000 genomes]
rs12536107	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12537487	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539942	0.82[AMR][1000 genomes]
rs12540797	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13229571	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13247186	0.87[ASN][1000 genomes]
rs28494902	0.88[ASN][1000 genomes]
rs28649084	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34857592	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34899283	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34947632	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35121012	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35291651	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35644498	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35768299	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62439721	0.86[AFR][1000 genomes]
rs62439727	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62439734	0.84[EUR][1000 genomes]
rs62439737	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62439738	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62439743	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6463579	0.90[ASN][1000 genomes]
rs6463580	0.90[ASN][1000 genomes]
rs6954172	0.90[ASN][1000 genomes]
rs7784521	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789640	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7792579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7792858	0.93[ASN][1000 genomes]
rs7796846	0.83[ASN][1000 genomes]
rs7804542	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv10861	chr7:6749172-6768435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1819632	chr7:6749937-6767410	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv966755	chr7:6750289-6769785	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv966754	chr7:6750289-6838266	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887442	chr7:6753286-6820508	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887443	chr7:6753286-6832265	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv887444	chr7:6753286-6855510	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv887445	chr7:6758018-6843722	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv887446	chr7:6758018-6870635	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv887447	chr7:6764583-6843722	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv887448	chr7:6764583-6855510	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv887449	chr7:6764583-6870635	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	esv2757207	chr7:6764583-6977214	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	esv2759504	chr7:6764583-6977214	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6747000-6768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6754600-6768600	Weak transcription	Liver	Liver
3	chr7:6763600-6766600	Enhancers	Primary B cells from cord blood	blood
4	chr7:6764000-6765800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr7:6764000-6766200	Enhancers	Primary B cells from peripheral blood	blood
6	chr7:6764200-6765800	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:6764200-6766200	Enhancers	GM12878-XiMat	blood
8	chr7:6764400-6765200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr7:6764400-6765400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:6764400-6765800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:6764600-6765200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:6764600-6765200	Enhancers	Spleen	Spleen
13	chr7:6764600-6765800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:6764800-6765000	Enhancers	Monocytes-CD14+_RO01746	blood

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