Variant report

Variant	rs4723884
Chromosome Location	chr7:39649275-39649276
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	SPI1	chr7:39649136-39649353	GM12878	blood:	n/a	n/a
2	EP300	chr7:39648599-39649302	SK-N-SH_RA	brain:	n/a	n/a
3	TEAD4	chr7:39648599-39649486	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr7:39648496-39649803	HUVEC	blood vessel:	n/a	n/a
5	CEBPB	chr7:39648667-39649318	IMR90	lung:	n/a	chr7:39648848-39648859
6	POLR2A	chr7:39648448-39650115	HUVEC	blood vessel:	n/a	n/a
7	MAX	chr7:39648612-39649540	SK-N-SH	brain:	n/a	chr7:39649309-39649319
8	TBP	chr7:39649144-39649625	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOSL2	chr7:39648629-39649361	SK-N-SH	brain:	n/a	n/a
10	UBTF	chr7:39649219-39649629	K562	blood:	n/a	n/a
11	NFIC	chr7:39648513-39649461	SK-N-SH	brain:	n/a	n/a
12	TAF1	chr7:39649038-39649306	SK-N-SH	brain:	n/a	n/a
13	RCOR1	chr7:39649099-39649367	K562	blood:	n/a	n/a
14	GATA2	chr7:39648591-39649940	SH-SY5Y	brain:	n/a	n/a
15	MAX	chr7:39649179-39649375	NB4	blood:	n/a	chr7:39649309-39649319
16	MAX	chr7:39649204-39649385	K562	blood:	n/a	chr7:39649309-39649319
17	EP300	chr7:39648492-39649331	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr7:39647722-39649489	SK-N-SH	brain:	n/a	n/a
19	TCF12	chr7:39648496-39649466	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr7:39649274-39649603	H1-hESC	embryonic stem cell:	n/a	n/a
21	JUND	chr7:39648481-39649357	SK-N-SH	brain:	n/a	chr7:39648528-39648538
22	PBX3	chr7:39648527-39649511	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr7:39649160-39649310	HRE	kidney:	n/a	n/a
24	CTCF	chr7:39649247-39649665	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOS	chr7:39647889-39649907	HUVEC	blood vessel:	n/a	chr7:39648528-39648538
26	PAX5	chr7:39649231-39649505	GM12892	blood:	n/a	n/a
27	GABPA	chr7:39649246-39649605	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr7:39648548-39649939	SK-N-SH	brain:	n/a	chr7:39649309-39649319
29	HMGN3	chr7:39649218-39649542	K562	blood:	n/a	n/a
30	E2F6	chr7:39649082-39649596	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr7:39648836-39649659	IMR90	lung:	n/a	n/a
32	JUND	chr7:39648586-39649387	SK-N-SH	brain:	n/a	n/a
33	MAX	chr7:39649213-39649421	K562	blood:	n/a	chr7:39649309-39649319
34	RAD21	chr7:39649192-39649604	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr7:39649108-39649570	H1-hESC	embryonic stem cell:	n/a	chr7:39649309-39649319
36	POLR2A	chr7:39647773-39650312	HUVEC	blood vessel:	n/a	n/a
37	EP300	chr7:39648461-39649526	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr7:39648607-39649409	SK-N-SH	brain:	n/a	n/a
39	MYC	chr7:39649230-39649368	H1-hESC	embryonic stem cell:	n/a	chr7:39649309-39649319
40	TEAD4	chr7:39648542-39649655	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr7:39647664-39650225	HUVEC	blood vessel:	n/a	n/a
42	SPI1	chr7:39648997-39649463	HL-60	blood:	n/a	n/a
43	GATA3	chr7:39647612-39650090	SK-N-SH	brain:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124 chr7:39648116-39648124
44	MYC	chr7:39649216-39649397	HUVEC	blood vessel:	n/a	chr7:39649309-39649319
45	MAX	chr7:39649182-39649596	K562	blood:	n/a	chr7:39649309-39649319
46	POLR2A	chr7:39649136-39649519	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr7:39649198-39649491	H1-hESC	embryonic stem cell:	n/a	n/a
48	GATA3	chr7:39647622-39649486	SK-N-SH	brain:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124 chr7:39648116-39648124
49	FOXP2	chr7:39649228-39649372	PFSK-1	brain:	n/a	n/a
50	GATA2	chr7:39647563-39649910	HUVEC	blood vessel:	n/a	chr7:39648117-39648124 chr7:39648352-39648361 chr7:39648349-39648365 chr7:39648222-39648232 chr7:39648115-39648124 chr7:39648117-39648124 chr7:39648350-39648363 chr7:39648117-39648124

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:39649254-39649304	T-47D	breast:	n/a
2	chr7:39649254-39649304	NB4	blood:	n/a
3	chr7:39649254-39649304	HUVEC	blood vessel:	n/a
4	chr7:39649254-39649304	GM12891	blood:	n/a
5	chr7:39649254-39649304	AG10803	skin:	n/a
6	chr7:39649254-39649304	SK-N-MC	brain:	n/a
7	chr7:39649254-39649304	MCF-7	breast:	n/a
8	chr7:39649254-39649304	Caco-2	colon:	n/a
9	chr7:39649254-39649304	BJ	skin:	n/a
10	chr7:39649254-39649304	PANC-1	pancreas:	n/a
11	chr7:39649254-39649304	AG09309	skin:	n/a
12	chr7:39649254-39649304	H1-hESC	embryonic stem cell:	embryo
13	chr7:39649254-39649304	HCT-116	colon:	n/a
14	chr7:39649254-39649304	SKMC	muscle:	n/a
15	chr7:39649254-39649304	NT2-D1	testis:	n/a
16	chr7:39649254-39649304	IMR90	lung:	fetal
17	chr7:39649254-39649304	Hela-S3	cervix:	n/a
18	chr7:39649254-39649304	GM12878	blood:	n/a
19	chr7:39649254-39649304	NHDF-neo	bronchial:	n/a
20	chr7:39649254-39649304	AoSMC	blood vessel:	n/a
21	chr7:39649254-39649304	GM19239	blood:	n/a
22	chr7:39649254-39649304	NH-A	brain:	n/a
23	chr7:39649254-39649304	HEEpiC	esophagus:	n/a
24	chr7:39649254-39649304	RPTEC	kidney:	n/a
25	chr7:39649254-39649304	HEK293	kidney:	embryo
26	chr7:39649254-39649304	A549	lung:	n/a
27	chr7:39649254-39649304	ProgFib	skin:	n/a
28	chr7:39649254-39649304	Jurkat	blood:	n/a
29	chr7:39649254-39649304	CMK	blood:	n/a
30	chr7:39649254-39649304	HepG2	liver:	n/a
31	chr7:39649254-39649304	SK-N-SH_RA	brain:	n/a
32	chr7:39649254-39649304	ECC-1	luminal epithelium:	n/a
33	chr7:39649254-39649304	GM06990	blood:	n/a
34	chr7:39649254-39649304	HL-60	blood:	n/a
35	chr7:39649254-39649304	LNCaP	prostate:	n/a
36	chr7:39649254-39649304	HMEC	breast:	n/a
37	chr7:39649254-39649304	HRCEpiC	kidney:	n/a
38	chr7:39649254-39649304	BE2_C	brain:	n/a
39	chr7:39649254-39649304	HIPEpiC	eye:	n/a
40	chr7:39649254-39649304	SK-N-SH	brain:	n/a
41	chr7:39649254-39649304	Hepatocyte	liver:	n/a
42	chr7:39649254-39649304	HAEpiC	amniotic membrane:	n/a
43	chr7:39649254-39649304	SAEC	small airway:	n/a
44	chr7:39649254-39649304	HCM	heart:	n/a
45	chr7:39649254-39649304	MCF10A-Er-Src	breast:	n/a
46	chr7:39649254-39649304	K562	blood:	n/a
47	chr7:39649254-39649304	HCPEpiC	choroid plexus:	n/a
48	chr7:39649254-39649304	HRPEpiC	eye:	n/a
49	chr7:39649254-39649304	NHBE	bronchial:	n/a
50	chr7:39649254-39649304	PrEC	prostate:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-6	chr7:39649209-39649494	ENSG00000231951.1
2	lnc-YAE1D1-1	chr7:39649086-39651687	NONHSAT120210

Variant related genes	Relation type
ENSG00000106540	TF binding region
ENSG00000106540	CpG island

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10245247	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258946	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266149	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap]
rs12111908	0.98[ASN][1000 genomes]
rs17171603	0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.82[ASN][1000 genomes]
rs17713951	0.86[ASN][1000 genomes]
rs17714049	0.98[ASN][1000 genomes]
rs17770594	0.82[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17770625	0.82[ASN][1000 genomes]
rs1989533	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329460	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329461	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4451213	0.82[AMR][1000 genomes]
rs4469364	0.90[AFR][1000 genomes]
rs4720329	0.92[AFR][1000 genomes]
rs4723881	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299139	0.82[ASN][1000 genomes]
rs59071947	0.82[ASN][1000 genomes]
rs61493712	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958662	0.93[AFR][1000 genomes]
rs6968742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375695	0.82[ASN][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs7785964	0.82[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]
rs7809088	0.93[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39644800-39649800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:39645200-39649400	Weak transcription	HSMMtube	muscle
3	chr7:39645200-39661600	Weak transcription	A549	lung
4	chr7:39646400-39650000	Enhancers	Stomach Mucosa	stomach
5	chr7:39647000-39649800	Enhancers	Hela-S3	cervix
6	chr7:39647600-39650000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:39647600-39650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr7:39647800-39649400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:39647800-39649400	Enhancers	Osteobl	bone
10	chr7:39647800-39649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:39648000-39649800	Enhancers	Small Intestine	intestine
12	chr7:39648000-39649800	Enhancers	HSMM	muscle
13	chr7:39648000-39650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:39648400-39651800	Flanking Active TSS	HUVEC	blood vessel
15	chr7:39648600-39649600	Flanking Active TSS	HMEC	breast
16	chr7:39648600-39649800	Enhancers	Spleen	Spleen
17	chr7:39648600-39649800	Flanking Active TSS	NH-A	brain
18	chr7:39648600-39650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr7:39648800-39656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:39649000-39649400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:39649000-39649400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:39649000-39649400	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr7:39649000-39649400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr7:39649000-39649600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr7:39649000-39649600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr7:39649000-39649600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr7:39649000-39649600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
28	chr7:39649000-39649600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:39649000-39649600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr7:39649000-39649600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:39649000-39649600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr7:39649000-39649600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:39649000-39649600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
34	chr7:39649000-39649600	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr7:39649000-39649600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr7:39649000-39649600	Active TSS	Fetal Kidney	kidney
37	chr7:39649000-39649600	Flanking Active TSS	Fetal Lung	lung
38	chr7:39649000-39649600	Enhancers	Fetal Muscle Trunk	muscle
39	chr7:39649000-39649800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr7:39649000-39649800	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr7:39649000-39649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr7:39649000-39649800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr7:39649000-39649800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:39649000-39649800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:39649000-39649800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr7:39649000-39649800	Enhancers	Fetal Heart	heart
49	chr7:39649000-39649800	Active TSS	Rectal Smooth Muscle	rectum
50	chr7:39649000-39649800	Active TSS	Right Atrium	heart

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