Variant report

Variant	rs3800822
Chromosome Location	chr7:66147149-66147150
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:453)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:453 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr7:66146684-66147278	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr7:66146764-66147490	MCF-7	breast:	n/a	n/a
3	POLR2A	chr7:66146723-66147652	HL-60	blood:	n/a	n/a
4	RAD21	chr7:66146709-66148035	IMR90	lung:	n/a	n/a
5	GABPA	chr7:66146767-66147556	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr7:66146842-66147244	PFSK-1	brain:	n/a	n/a
7	REST	chr7:66146835-66147352	SK-N-SH	brain:	n/a	n/a
8	CCNT2	chr7:66146708-66147651	K562	blood:	n/a	n/a
9	POLR2A	chr7:66146716-66148139	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr7:66146015-66148114	GM12878	blood:	n/a	n/a
11	REST	chr7:66146859-66147198	PANC-1	pancreas:	n/a	n/a
12	GABPA	chr7:66146655-66147290	HepG2	liver:	n/a	n/a
13	EGR1	chr7:66146805-66147365	K562	blood:	n/a	chr7:66147019-66147028 chr7:66147302-66147312
14	POLR2A	chr7:66146758-66147399	HepG2	liver:	n/a	n/a
15	TAL1	chr7:66146816-66147260	K562	blood:	n/a	n/a
16	JUND	chr7:66146780-66147488	K562	blood:	n/a	n/a
17	POLR2A	chr7:66146592-66147529	PBDE	blood:	n/a	n/a
18	ATF2	chr7:66146428-66147281	GM12878	blood:	n/a	n/a
19	EGR1	chr7:66146773-66147463	MCF-7	breast:	n/a	chr7:66147019-66147028 chr7:66147302-66147312
20	FOXA2	chr7:66146590-66147400	A549	lung:	n/a	n/a
21	TAF1	chr7:66146739-66147425	K562	blood:	n/a	n/a
22	MXI1	chr7:66146525-66148833	IMR90	lung:	n/a	n/a
23	RAD21	chr7:66146677-66147547	SK-N-SH_RA	brain:	n/a	n/a
24	BHLHE40	chr7:66146781-66147502	GM12878	blood:	n/a	n/a
25	POU2F2	chr7:66146688-66147417	GM12891	blood:	n/a	chr7:66147299-66147311
26	RCOR1	chr7:66146494-66147778	K562	blood:	n/a	n/a
27	IRF1	chr7:66146845-66147463	K562	blood:	n/a	n/a
28	GABPA	chr7:66146617-66147292	A549	lung:	n/a	n/a
29	PML	chr7:66146747-66147483	MCF-7	breast:	n/a	n/a
30	PML	chr7:66146655-66147422	K562	blood:	n/a	n/a
31	TAF1	chr7:66146634-66147404	H1-neurons	neurons:	n/a	n/a
32	BCL3	chr7:66146800-66147433	A549	lung:	n/a	chr7:66147274-66147287 chr7:66146867-66146876
33	TAF1	chr7:66146617-66147613	A549	lung:	n/a	n/a
34	SIN3AK20	chr7:66146836-66147708	H1-hESC	embryonic stem cell:	n/a	n/a
35	GABPA	chr7:66146674-66147347	HepG2	liver:	n/a	n/a
36	GABPA	chr7:66146716-66147436	HL-60	blood:	n/a	n/a
37	EP300	chr7:66146768-66147309	A549	lung:	n/a	chr7:66146868-66146875
38	REST	chr7:66146707-66147339	SK-N-SH	brain:	n/a	n/a
39	MYC	chr7:66146674-66147394	K562	blood:	n/a	n/a
40	NFIC	chr7:66146763-66147267	ECC-1	luminal epithelium:	n/a	n/a
41	MYBL2	chr7:66146655-66147384	HepG2	liver:	n/a	n/a
42	POLR2A	chr7:66146078-66147376	GM12891	blood:	n/a	n/a
43	YY1	chr7:66146843-66147237	GM12891	blood:	n/a	chr7:66146918-66146929
44	NANOG	chr7:66146921-66147257	H1-hESC	embryonic stem cell:	n/a	n/a
45	CREB1	chr7:66146578-66147595	K562	blood:	n/a	n/a
46	POLR2A	chr7:66146333-66147705	K562	blood:	n/a	n/a
47	ZNF263	chr7:66146664-66147634	HEK293-T-REx	kidney:	n/a	n/a
48	ATF2	chr7:66146901-66147280	GM12878	blood:	n/a	n/a
49	TAF1	chr7:66146641-66147311	K562	blood:	n/a	n/a
50	NFIC	chr7:66146689-66147182	HepG2	liver:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:66145930..66148922-chr7:66213233..66215140,2	MCF-7	breast:
2	chr7:66146728..66147607-chr7:66205638..66206158,2	NB4	blood:
3	chr7:66118152..66121117-chr7:66145225..66147766,4	MCF-7	breast:
4	chr7:66145800..66148420-chr7:66309175..66311369,3	MCF-7	breast:
5	chr5:149829161..149829687-chr7:66146493..66147190,2	Hela-S3	cervix:
6	chr1:180123619..180124402-chr7:66147119..66147881,2	NB4	blood:
7	chr1:25573287..25574307-chr7:66146290..66147502,3	Hela-S3	cervix:
8	chr7:66144717..66148625-chr7:66203954..66207507,5	K562	blood:
9	chr7:66147119..66147718-chr7:66386034..66386593,2	Hela-S3	cervix:
10	chr7:66118965..66120049-chr7:66146710..66147584,5	MCF-7	breast:
11	chr7:66145819..66148736-chr7:66203770..66205462,3	MCF-7	breast:
12	chr7:66119490..66121348-chr7:66145844..66148158,2	K562	blood:
13	chr19:38826520..38827474-chr7:66146585..66147505,2	Hela-S3	cervix:
14	chr7:66144687..66148625-chr7:66203954..66207507,6	K562	blood:
15	chr19:49468432..49469010-chr7:66147016..66147572,2	Hela-S3	cervix:
16	chr7:66119464..66119965-chr7:66146773..66147348,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RABGEF1-3	chr7:66147078-66147245	NR_104676
2	lnc-RABGEF1-3	chr7:66147132-66147245	NONHSAT121219

No data

Variant related genes	Relation type
RABGEF1	TF binding region
ENSG00000087086	Chromatin interaction
ENSG00000164587	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000117616	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000230583	Chromatin interaction
ENSG00000271064	Chromatin interaction
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1267817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1267818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1267820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13228779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13232193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13235282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13236129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1573944	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1618893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1638736	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1882655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2178742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2659913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking 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 miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv981398	chr7:66138644-66147890	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3800822	GUSB	cis	Whole Blood	GTEx
rs3800822	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs3800822	RP4-756H11.3	cis	lung	GTEx
rs3800822	VKORC1L1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66146000-66147400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:66146000-66147600	Active TSS	Stomach Smooth Muscle	stomach
3	chr7:66146000-66147800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr7:66146000-66147800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr7:66146000-66148200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:66146000-66148400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:66146000-66148400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:66146000-66148400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:66146000-66148800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr7:66146000-66149200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:66146200-66147800	Active TSS	Liver	Liver
12	chr7:66146200-66148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:66146200-66148000	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr7:66146200-66148200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr7:66146200-66148200	Active TSS	Psoas Muscle	Psoas
16	chr7:66146200-66148400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr7:66146200-66148600	Active TSS	Rectal Smooth Muscle	rectum
18	chr7:66146200-66148600	Active TSS	GM12878-XiMat	blood
19	chr7:66146200-66149000	Active TSS	HSMM	muscle
20	chr7:66146400-66147200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:66146400-66147400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:66146400-66147800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:66146400-66147800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:66146400-66147800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr7:66146400-66147800	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr7:66146400-66147800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:66146400-66147800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:66146400-66147800	Active TSS	Fetal Intestine Large	intestine
29	chr7:66146400-66147800	Active TSS	Fetal Intestine Small	intestine
30	chr7:66146400-66147800	Active TSS	Pancreas	Pancrea
31	chr7:66146400-66147800	Active TSS	Stomach Mucosa	stomach
32	chr7:66146400-66147800	Active TSS	K562	blood
33	chr7:66146400-66148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:66146400-66148000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:66146400-66148000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr7:66146400-66148000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:66146400-66148000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:66146400-66148000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:66146400-66148000	Active TSS	Aorta	Aorta
40	chr7:66146400-66148000	Active TSS	Brain Substantia Nigra	brain
41	chr7:66146400-66148000	Active TSS	Left Ventricle	heart
42	chr7:66146400-66148200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr7:66146400-66148200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:66146400-66148200	Active TSS	Fetal Kidney	kidney
45	chr7:66146400-66148200	Active TSS	Gastric	stomach
46	chr7:66146400-66148200	Active TSS	Ovary	ovary
47	chr7:66146400-66148200	Active TSS	A549	lung
48	chr7:66146400-66148400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr7:66146400-66148400	Active TSS	Esophagus	oesophagus
50	chr7:66146400-66148600	Active TSS	Duodenum Smooth Muscle	Duodenum

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