Variant report

Variant	rs2492323
Chromosome Location	chr1:59365079-59365080
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:138)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:138 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TRIM28	chr1:59364460-59365503	K562	blood:	n/a	n/a
2	MAX	chr1:59364651-59365337	HepG2	liver:	n/a	n/a
3	JUND	chr1:59364701-59365140	HepG2	liver:	n/a	n/a
4	MAZ	chr1:59364485-59365417	K562	blood:	n/a	n/a
5	REST	chr1:59364644-59365397	K562	blood:	n/a	n/a
6	ZNF143	chr1:59364501-59365330	K562	blood:	n/a	chr1:59364599-59364608
7	SP1	chr1:59364605-59365300	HepG2	liver:	n/a	n/a
8	CEBPD	chr1:59364565-59365454	K562	blood:	n/a	n/a
9	FOXA1	chr1:59364588-59365371	HepG2	liver:	n/a	n/a
10	MXI1	chr1:59364666-59365187	K562	blood:	n/a	n/a
11	FOXA1	chr1:59364601-59365298	HepG2	liver:	n/a	n/a
12	REST	chr1:59364676-59365303	K562	blood:	n/a	n/a
13	CUX1	chr1:59364568-59365962	K562	blood:	n/a	n/a
14	POLR2A	chr1:59364523-59365433	K562	blood:	n/a	n/a
15	RFX5	chr1:59364742-59365244	HepG2	liver:	n/a	n/a
16	MAX	chr1:59364595-59365492	K562	blood:	n/a	n/a
17	STAT5A	chr1:59364513-59365446	K562	blood:	n/a	n/a
18	GATA1	chr1:59364412-59365541	PBDE	blood:	n/a	n/a
19	CBX3	chr1:59364672-59365378	K562	blood:	n/a	n/a
20	CREB1	chr1:59364306-59365458	K562	blood:	n/a	n/a
21	EP300	chr1:59364272-59365334	K562	blood:	n/a	chr1:59364686-59364695
22	HNF4A	chr1:59364670-59365312	HepG2	liver:	n/a	chr1:59364975-59364990
23	TBL1XR1	chr1:59364578-59365747	K562	blood:	n/a	n/a
24	CCNT2	chr1:59364581-59365400	K562	blood:	n/a	n/a
25	TBP	chr1:59364669-59365254	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:59364592-59365274	K562	blood:	n/a	n/a
27	USF1	chr1:59364564-59365327	K562	blood:	n/a	chr1:59364863-59364874
28	NFIC	chr1:59364637-59365148	HepG2	liver:	n/a	n/a
29	GATA1	chr1:59364657-59365359	K562	blood:	n/a	n/a
30	SP1	chr1:59364568-59365195	K562	blood:	n/a	n/a
31	ELF1	chr1:59364565-59365398	K562	blood:	n/a	n/a
32	JUN	chr1:59364236-59365333	K562	blood:	n/a	chr1:59364470-59364484
33	RAD21	chr1:59364674-59365138	HepG2	liver:	n/a	n/a
34	GATA1	chr1:59364678-59365235	PBDEFetal	blood:	n/a	n/a
35	TBL1XR1	chr1:59364613-59365494	K562	blood:	n/a	n/a
36	TEAD4	chr1:59364393-59365559	K562	blood:	n/a	n/a
37	MAX	chr1:59364425-59365420	K562	blood:	n/a	n/a
38	BHLHE40	chr1:59364618-59365282	HepG2	liver:	n/a	n/a
39	GATA2	chr1:59364606-59365362	K562	blood:	n/a	n/a
40	CEBPB	chr1:59364389-59365262	K562	blood:	n/a	chr1:59364579-59364590 chr1:59364578-59364591
41	MAX	chr1:59364581-59365659	NB4	blood:	n/a	n/a
42	EP300	chr1:59364610-59365282	HepG2	liver:	n/a	chr1:59364686-59364695
43	TEAD4	chr1:59364575-59365223	HepG2	liver:	n/a	n/a
44	NFIC	chr1:59364637-59365184	HepG2	liver:	n/a	n/a
45	MAFK	chr1:59364400-59365377	K562	blood:	n/a	n/a
46	JUN	chr1:59364562-59365265	K562	blood:	n/a	n/a
47	EGR1	chr1:59364611-59365277	K562	blood:	n/a	n/a
48	USF1	chr1:59364660-59365126	HepG2	liver:	n/a	chr1:59364863-59364874
49	RCOR1	chr1:59364341-59365547	K562	blood:	n/a	n/a
50	ATF1	chr1:59364679-59365417	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59335945..59337936-chr1:59364743..59367099,2	K562	blood:
2	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
3	chr1:59363087..59366662-chr1:59367277..59371776,8	K562	blood:
4	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
5	chr1:59364854..59367542-chr1:59372083..59374801,2	K562	blood:
6	chr1:59316456..59319340-chr1:59363706..59366262,2	K562	blood:
7	chr1:59285707..59288503-chr1:59364904..59368288,3	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGGY-5	chr1:59364719-59365265	ENSG00000234807
2	lnc-FGGY-5	chr1:59364719-59365384	ENSG00000234807
3	lnc-FGGY-5	chr1:59364719-59365384	NONHSAT003524
4	lnc-FGGY-5	chr1:59364719-59365266	NONHSAT003525
5	lnc-FGGY-5	chr1:59364719-59365384	NR_108106
6	lnc-FGGY-5	chr1:59364719-59365266	ENSG00000234807.4

No data

Variant related genes	Relation type
ENSG00000232453	TF binding region
ENSG00000231740	Chromatin interaction
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1998761	0.85[AMR][1000 genomes]
rs1998762	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2011623	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2492321	0.86[CHB][hapmap];0.95[YRI][hapmap]
rs2764908	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2999129	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59356200-59368600	Weak transcription	Esophagus	oesophagus
2	chr1:59358200-59367200	Enhancers	HUVEC	blood vessel
3	chr1:59358400-59368600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:59358600-59367000	Enhancers	Adipose Nuclei	Adipose
5	chr1:59358800-59365800	Enhancers	Lung	lung
6	chr1:59358800-59367000	Enhancers	Fetal Muscle Leg	muscle
7	chr1:59359000-59365800	Enhancers	Left Ventricle	heart
8	chr1:59359000-59366400	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:59359000-59367000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
12	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
13	chr1:59359200-59366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:59359600-59365600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:59359600-59365600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:59360000-59367000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:59360600-59365400	Enhancers	Spleen	Spleen
18	chr1:59360600-59366600	Enhancers	Colonic Mucosa	Colon
19	chr1:59361000-59366600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:59361200-59367000	Enhancers	Ovary	ovary
21	chr1:59361200-59368800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:59361600-59367000	Enhancers	Fetal Lung	lung
23	chr1:59361600-59368400	Weak transcription	GM12878-XiMat	blood
24	chr1:59361800-59368800	Weak transcription	HMEC	breast
25	chr1:59362000-59366000	Weak transcription	Osteobl	bone
26	chr1:59362200-59366600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:59362400-59368600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:59362400-59368600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:59362400-59368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:59362400-59369000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:59362600-59368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:59362600-59368800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:59362600-59368800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:59362800-59367800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:59362800-59367800	Weak transcription	Fetal Thymus	thymus
36	chr1:59362800-59368600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:59362800-59368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:59362800-59368800	Weak transcription	NH-A	brain
39	chr1:59362800-59368800	Weak transcription	NHEK	skin
40	chr1:59362800-59369000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:59362800-59369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:59363000-59365800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:59363000-59366000	Weak transcription	NHDF-Ad	bronchial
44	chr1:59363000-59366200	Weak transcription	NHLF	lung
45	chr1:59363200-59366800	Weak transcription	Hela-S3	cervix
46	chr1:59363200-59368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:59363200-59368600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:59363200-59369000	Weak transcription	Brain Angular Gyrus	brain
49	chr1:59363400-59365800	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:59363600-59365200	Weak transcription	HSMMtube	muscle

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