Variant report

Variant	rs2887640
Chromosome Location	chr1:193027834-193027835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:314)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:314 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr1:193027595-193027917	Hela-S3	cervix:	n/a	n/a
2	PAX5	chr1:193027589-193028109	GM12878	blood:	n/a	n/a
3	POU2F2	chr1:193027580-193027998	GM12878	blood:	n/a	n/a
4	MYC	chr1:193027732-193028134	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:193027498-193028074	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr1:193027820-193027970	SAEC	small airway:	n/a	n/a
7	RCOR1	chr1:193027249-193030002	IMR90	lung:	n/a	n/a
8	CTCF	chr1:193027713-193027952	GM12878	blood:	n/a	n/a
9	MYC	chr1:193026894-193029449	K562	blood:	n/a	n/a
10	POLR2A	chr1:193027597-193028046	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:193027639-193029062	GM12878	blood:	n/a	n/a
12	MAX	chr1:193027458-193029459	SK-N-SH	brain:	n/a	n/a
13	PML	chr1:193027331-193029093	K562	blood:	n/a	n/a
14	EP300	chr1:193027603-193029005	GM12878	blood:	n/a	chr1:193028433-193028449 chr1:193028436-193028452
15	POLR2A	chr1:193027599-193027946	HUVEC	blood vessel:	n/a	n/a
16	ELF1	chr1:193027523-193027925	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:193027435-193029267	GM12891	blood:	n/a	n/a
18	BATF	chr1:193027626-193027903	GM12878	blood:	n/a	n/a
19	ELF1	chr1:193027598-193027955	K562	blood:	n/a	n/a
20	POLR2A	chr1:193027385-193029406	HepG2	liver:	n/a	n/a
21	POU2F2	chr1:193027553-193029274	GM12891	blood:	n/a	chr1:193028437-193028449
22	TAF1	chr1:193027531-193028109	K562	blood:	n/a	n/a
23	STAT5A	chr1:193027375-193029470	K562	blood:	n/a	n/a
24	HCFC1	chr1:193027359-193029333	K562	blood:	n/a	n/a
25	MYBL2	chr1:193027586-193029039	HepG2	liver:	n/a	n/a
26	TBP	chr1:193027512-193027981	Hela-S3	cervix:	n/a	n/a
27	RELA	chr1:193027553-193029329	GM15510	blood:	n/a	n/a
28	CREB1	chr1:193027362-193029761	K562	blood:	n/a	n/a
29	HEY1	chr1:193027535-193028151	HepG2	liver:	n/a	n/a
30	EGR1	chr1:193027642-193027895	GM12878	blood:	n/a	chr1:193027764-193027777 chr1:193027765-193027775
31	CEBPD	chr1:193027536-193029230	K562	blood:	n/a	n/a
32	SPI1	chr1:193027618-193027955	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:193027395-193029342	NB4	blood:	n/a	n/a
34	JUND	chr1:193027592-193029404	K562	blood:	n/a	chr1:193028660-193028671 chr1:193028223-193028232
35	TAF1	chr1:193027344-193028954	PFSK-1	brain:	n/a	n/a
36	TBP	chr1:193027476-193027995	GM12878	blood:	n/a	n/a
37	CTCF	chr1:193027700-193027850	AG10803	skin:	n/a	n/a
38	MAZ	chr1:193027249-193029462	IMR90	lung:	n/a	n/a
39	MXI1	chr1:193027440-193030657	IMR90	lung:	n/a	n/a
40	POLR2A	chr1:193027524-193029324	HL-60	blood:	n/a	n/a
41	REST	chr1:193027452-193029791	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr1:193027436-193029598	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr1:193027520-193029476	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr1:193027360-193027965	K562	blood:	n/a	n/a
45	CBX3	chr1:193027230-193029244	K562	blood:	n/a	n/a
46	TAF1	chr1:193027589-193028083	GM12891	blood:	n/a	n/a
47	BHLHE40	chr1:193027074-193029279	K562	blood:	n/a	chr1:193028446-193028462 chr1:193028435-193028451 chr1:193028443-193028459
48	CTCF	chr1:193027740-193027890	WERI-Rb-1	eye:	n/a	n/a
49	ELK4	chr1:193027537-193028116	Hela-S3	cervix:	n/a	chr1:193027716-193027725 chr1:193027716-193027724 chr1:193027715-193027726
50	CREB1	chr1:193027310-193029409	K562	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:193025349..193030732-chr1:193089240..193093287,15	MCF-7	breast:
2	chr1:193026932..193030661-chr1:193071909..193075798,10	K562	blood:
3	chr1:192996006..192999093-chr1:193026171..193028166,3	K562	blood:
4	chr1:192777305..192779700-chr1:193027165..193029983,2	K562	blood:
5	chr1:192993820..193002591-chr1:193021038..193030016,12	K562	blood:
6	chr1:153539269..153539769-chr1:193027651..193028285,2	Hela-S3	cervix:
7	chr1:193025655..193031465-chr1:193087281..193093381,17	MCF-7	breast:
8	chr1:193027166..193030257-chr1:193073439..193079424,9	MCF-7	breast:
9	chr1:186341227..186346056-chr1:193025925..193030298,4	K562	blood:
10	chr1:193020543..193046917-chr1:193069266..193098746,125	K562	blood:
11	chr1:193018810..193043703-chr1:193079188..193098601,93	K562	blood:
12	chr1:193027586..193031673-chr1:193072686..193075563,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238754	TF binding region
TROVE2	TF binding region
ENSG00000023572	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000116741	Chromatin interaction
ENSG00000157181	Chromatin interaction
ENSG00000134371	Chromatin interaction
ENSG00000116750	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10489686	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10494675	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10801170	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10801186	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12118724	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12119992	1.00[CEU][hapmap]
rs12122868	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12123511	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12123750	1.00[CEU][hapmap]
rs12123970	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12129832	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12132305	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134846	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12135148	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12135670	1.00[CEU][hapmap]
rs12136893	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12141029	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12145101	0.85[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1325196	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17526825	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17592121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17593120	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs28930673	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs28930674	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs34961778	0.82[AMR][1000 genomes]
rs35221108	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56022114	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6670264	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6682904	1.00[CEU][hapmap]
rs72738588	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72738589	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72738599	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7415619	1.00[GIH][hapmap]
rs7544830	0.89[EUR][1000 genomes]
rs842805	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription 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 miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193026200-193028200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr1:193026600-193029800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:193026600-193030200	Active TSS	K562	blood
4	chr1:193026600-193030800	Active TSS	NHLF	lung
5	chr1:193026800-193028000	Flanking Active TSS	HUVEC	blood vessel
6	chr1:193026800-193028400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:193026800-193030000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:193026800-193030200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:193026800-193031000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:193027000-193028000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:193027000-193028000	Flanking Active TSS	Fetal Brain Female	brain
12	chr1:193027000-193028200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:193027000-193028200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:193027000-193028200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:193027000-193030000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:193027000-193030000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:193027000-193030000	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr1:193027000-193030000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr1:193027000-193030000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:193027000-193030000	Active TSS	A549	lung
21	chr1:193027000-193030200	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr1:193027000-193030200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:193027000-193030200	Active TSS	Right Ventricle	heart
24	chr1:193027000-193030800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:193027000-193032600	Active TSS	GM12878-XiMat	blood
26	chr1:193027200-193028000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr1:193027200-193028200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:193027200-193028200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr1:193027200-193028200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:193027200-193028400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:193027200-193028400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr1:193027200-193028400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:193027200-193029800	Active TSS	Fetal Intestine Small	intestine
34	chr1:193027200-193030200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:193027200-193030200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:193027200-193030200	Active TSS	HMEC	breast
37	chr1:193027200-193030600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:193027200-193031000	Active TSS	HSMM	muscle
39	chr1:193027400-193028000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:193027400-193028000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:193027400-193028000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr1:193027400-193028000	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr1:193027400-193028000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr1:193027400-193028000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:193027400-193028000	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr1:193027400-193028000	Flanking Active TSS	Fetal Brain Male	brain
47	chr1:193027400-193028000	Flanking Active TSS	NH-A	brain
48	chr1:193027400-193028200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr1:193027400-193028200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr1:193027400-193028200	Flanking Active TSS	Primary hematopoietic stem cells	blood

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