Variant report

Variant	rs3811465
Chromosome Location	chr1:222886119-222886120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:444)
CpG islands
(count:122)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:444 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr1:222885678-222886355	MCF-7	breast:	n/a	n/a
2	TAF1	chr1:222885621-222886992	GM12878	blood:	n/a	n/a
3	USF1	chr1:222885736-222886758	H1-hESC	embryonic stem cell:	n/a	n/a
4	PAX5	chr1:222885826-222886212	GM12878	blood:	n/a	n/a
5	YY1	chr1:222885690-222887002	K562	blood:	n/a	n/a
6	PML	chr1:222885681-222887057	K562	blood:	n/a	chr1:222886762-222886770
7	E2F6	chr1:222884665-222887010	K562	blood:	n/a	chr1:222886650-222886659 chr1:222885810-222885818
8	SIX5	chr1:222885835-222886299	K562	blood:	n/a	n/a
9	SRF	chr1:222886020-222886232	GM12878	blood:	n/a	n/a
10	MYC	chr1:222884615-222886950	K562	blood:	n/a	chr1:222886670-222886680
11	TCF12	chr1:222885681-222887190	A549	lung:	n/a	n/a
12	POLR2A	chr1:222884479-222887260	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:222885564-222886959	U87	brain:	n/a	n/a
14	ATF3	chr1:222885891-222886814	A549	lung:	n/a	n/a
15	POLR2A	chr1:222885406-222886224	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAZ	chr1:222885773-222887381	GM12878	blood:	n/a	chr1:222886670-222886680
17	MAX	chr1:222885725-222886961	MCF-7	breast:	n/a	chr1:222886670-222886680
18	POLR2A	chr1:222885243-222886293	GM12878	blood:	n/a	n/a
19	ATF3	chr1:222886029-222886153	GM12878	blood:	n/a	n/a
20	SIN3A	chr1:222884727-222887390	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF384	chr1:222885922-222886989	K562	blood:	n/a	n/a
22	SMC3	chr1:222885841-222886999	Hela-S3	cervix:	n/a	chr1:222886667-222886677
23	TAF1	chr1:222885690-222886336	SK-N-SH	brain:	n/a	n/a
24	CHD2	chr1:222885977-222886947	H1-hESC	embryonic stem cell:	n/a	n/a
25	ELF1	chr1:222885733-222887068	SK-N-SH	brain:	n/a	n/a
26	USF1	chr1:222885734-222886851	ECC-1	luminal epithelium:	n/a	n/a
27	E2F4	chr1:222885528-222886840	MCF10A-Er-Src	breast:	n/a	chr1:222886650-222886659 chr1:222885810-222885818
28	ELF1	chr1:222885709-222887352	HCT-116	colon:	n/a	n/a
29	SIX5	chr1:222885760-222886363	A549	lung:	n/a	n/a
30	MAX	chr1:222885713-222886982	ECC-1	luminal epithelium:	n/a	chr1:222886670-222886680
31	ATF2	chr1:222885936-222886837	H1-hESC	embryonic stem cell:	n/a	n/a
32	BRCA1	chr1:222885970-222886272	GM12878	blood:	n/a	n/a
33	ZMIZ1	chr1:222884806-222887257	K562	blood:	n/a	n/a
34	MYBL2	chr1:222885882-222887052	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:222885142-222887096	GM12892	blood:	n/a	n/a
36	TAF1	chr1:222885619-222886213	HepG2	liver:	n/a	n/a
37	YY1	chr1:222885701-222886806	H1-hESC	embryonic stem cell:	n/a	n/a
38	STAT1	chr1:222885827-222887019	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:222884702-222887083	GM19193	blood:	n/a	n/a
40	HA-E2F1	chr1:222885346-222886877	Hela-S3	cervix:	n/a	chr1:222886650-222886659
41	POLR2A	chr1:222885093-222886361	GM12878	blood:	n/a	n/a
42	SMARCB1	chr1:222884770-222887237	Hela-S3	cervix:	n/a	n/a
43	ELF1	chr1:222885682-222887242	HepG2	liver:	n/a	n/a
44	ATF3	chr1:222885880-222886377	HepG2	liver:	n/a	n/a
45	CTCF	chr1:222885971-222886995	K562	blood:	n/a	n/a
46	ELF1	chr1:222885666-222887118	GM12878	blood:	n/a	n/a
47	SIX5	chr1:222885864-222886262	K562	blood:	n/a	n/a
48	USF1	chr1:222885828-222886358	A549	lung:	n/a	n/a
49	POLR2A	chr1:222885688-222887110	HCT-116	colon:	n/a	n/a
50	POLR2A	chr1:222884689-222887187	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:222886073-222886123	LNCaP	prostate:	n/a
2	chr1:222886073-222886123	AG09319	gingival:	n/a
3	chr1:222886073-222886123	PFSK-1	brain:	n/a
4	chr1:222886073-222886123	AG04449	skin:	fetal
5	chr1:222886073-222886123	NHBE	bronchial:	n/a
6	chr1:222886071-222886121	HAEpiC	amniotic membrane:	n/a
7	chr1:222886071-222886121	PrEC	prostate:	n/a
8	chr1:222886071-222886121	HCT-116	colon:	n/a
9	chr1:222886073-222886123	SK-N-MC	brain:	n/a
10	chr1:222886073-222886123	HCPEpiC	choroid plexus:	n/a
11	chr1:222886073-222886123	H1-hESC	embryonic stem cell:	embryo
12	chr1:222886071-222886121	GM12892	blood:	n/a
13	chr1:222886073-222886123	Hela-S3	cervix:	n/a
14	chr1:222886073-222886123	GM12878	blood:	n/a
15	chr1:222886073-222886123	GM12892	blood:	n/a
16	chr1:222886071-222886121	HCF	heart:	n/a
17	chr1:222886073-222886123	Hepatocyte	liver:	n/a
18	chr1:222886073-222886123	SK-N-SH	brain:	n/a
19	chr1:222886073-222886123	BE2_C	brain:	n/a
20	chr1:222886073-222886123	A549	lung:	n/a
21	chr1:222886071-222886121	HCPEpiC	choroid plexus:	n/a
22	chr1:222886071-222886121	AG04450	lung:	fetal
23	chr1:222886073-222886123	PrEC	prostate:	n/a
24	chr1:222886073-222886123	SK-N-SH_RA	brain:	n/a
25	chr1:222886073-222886123	BJ	skin:	n/a
26	chr1:222886073-222886123	GM19239	blood:	n/a
27	chr1:222886073-222886123	CMK	blood:	n/a
28	chr1:222886071-222886121	HUVEC	blood vessel:	n/a
29	chr1:222886073-222886123	T-47D	breast:	n/a
30	chr1:222886073-222886123	Jurkat	blood:	n/a
31	chr1:222886073-222886123	HPAEpiC	pulmonary alveolar:	n/a
32	chr1:222886073-222886123	U87	brain:	n/a
33	chr1:222886071-222886121	PANC-1	pancreas:	n/a
34	chr1:222886073-222886123	HepG2	liver:	n/a
35	chr1:222886073-222886123	GM12891	blood:	n/a
36	chr1:222886073-222886123	NB4	blood:	n/a
37	chr1:222886073-222886123	HRE	kidney:	n/a
38	chr1:222886071-222886121	MCF10A-Er-Src	breast:	n/a
39	chr1:222886071-222886121	AG04449	skin:	fetal
40	chr1:222886071-222886121	Hela-S3	cervix:	n/a
41	chr1:222886071-222886121	H1-hESC	embryonic stem cell:	embryo
42	chr1:222886071-222886121	PFSK-1	brain:	n/a
43	chr1:222886073-222886123	HRPEpiC	eye:	n/a
44	chr1:222886073-222886123	MCF10A-Er-Src	breast:	n/a
45	chr1:222886071-222886121	Hepatocyte	liver:	n/a
46	chr1:222886071-222886121	NT2-D1	testis:	n/a
47	chr1:222886071-222886121	HIPEpiC	eye:	n/a
48	chr1:222886071-222886121	BE2_C	brain:	n/a
49	chr1:222886073-222886123	HEEpiC	esophagus:	n/a
50	chr1:222886071-222886121	SK-N-SH_RA	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
2	chr1:222836221..222837854-chr1:222884380..222886530,2	MCF-7	breast:
3	chr1:222814795..222819438-chr1:222884035..222887873,13	K562	blood:
4	chr1:222849453..222853444-chr1:222884619..222888596,6	K562	blood:
5	chr1:222837235..222840536-chr1:222884708..222887368,3	MCF-7	breast:
6	chr1:222886023..222886943-chr17:1552762..1553506,2	Hela-S3	cervix:
7	chr1:222886029..222886690-chr3:156878406..156878911,2	Hela-S3	cervix:
8	chr1:222817680..222819791-chr1:222885041..222887043,2	MCF-7	breast:
9	chr1:222789930..222793106-chr1:222884660..222888170,6	K562	blood:
10	chr1:222790149..222792584-chr1:222885363..222887404,2	K562	blood:
11	chr1:222885691..222887842-chr17:56707440..56710300,2	MCF-7	breast:
12	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
13	chr1:222885721..222886410-chr4:120987809..120988640,2	HCT-116	colon:
14	chr1:222885445..222886358-chr3:15643061..15643643,2	Hela-S3	cervix:
15	chr1:222886038..222886696-chr10:101380647..101381633,2	Hela-S3	cervix:
16	chr1:222815622..222820703-chr1:222883498..222888165,14	K562	blood:

No data

Variant related genes	Relation type
AIDA	TF binding region
BROX	TF binding region
RN7SL276P	TF binding region
AIDA	CpG island
RN7SL276P	CpG island
BROX	CpG island
ENSG00000250938	Chromatin interaction
ENSG00000167705	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000225265	Chromatin interaction
ENSG00000169814	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000143498	Chromatin interaction
ENSG00000131373	Chromatin interaction
ENSG00000229399	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000260475	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11485123	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12063226	0.94[EUR][1000 genomes]
rs1391557	0.88[EUR][1000 genomes]
rs1391558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1498382	0.88[EUR][1000 genomes]
rs17011666	0.95[MEX][hapmap]
rs17011686	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[ASN][1000 genomes]
rs17163337	0.85[JPT][hapmap]
rs17163450	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs17163468	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs2030076	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2088514	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2133188	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2270707	1.00[MEX][hapmap]
rs2378604	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936020	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936023	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2936049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2936051	0.83[EUR][1000 genomes]
rs2936052	0.83[EUR][1000 genomes]
rs2936054	0.82[EUR][1000 genomes]
rs3002129	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3002146	0.88[EUR][1000 genomes]
rs3002148	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3008614	0.82[EUR][1000 genomes]
rs3008615	0.82[EUR][1000 genomes]
rs3008616	0.82[EUR][1000 genomes]
rs3008618	0.83[EUR][1000 genomes]
rs3008622	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3008625	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3008629	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008637	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34433664	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35507977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61824336	0.91[AFR][1000 genomes]
rs61827168	0.83[EUR][1000 genomes]
rs6683071	0.80[ASW][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3811465	C1orf58	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222883200-222887600	Active TSS	Brain Anterior Caudate	brain
2	chr1:222883800-222887400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:222883800-222887600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:222883800-222887600	Active TSS	Fetal Kidney	kidney
5	chr1:222883800-222887600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:222883800-222887600	Active TSS	NHLF	lung
7	chr1:222883800-222887800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:222883800-222887800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:222883800-222888000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:222883800-222888000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:222884000-222887200	Active TSS	Brain Angular Gyrus	brain
12	chr1:222884000-222887400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:222884000-222887400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:222884000-222887600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:222884000-222887600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:222884000-222887600	Active TSS	Fetal Intestine Small	intestine
17	chr1:222884000-222887600	Active TSS	Ovary	ovary
18	chr1:222884000-222887600	Active TSS	Right Atrium	heart
19	chr1:222884000-222887600	Active TSS	A549	lung
20	chr1:222884000-222887600	Active TSS	GM12878-XiMat	blood
21	chr1:222884000-222887600	Active TSS	HSMM	muscle
22	chr1:222884000-222887800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:222884000-222887800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:222884200-222887200	Active TSS	Hela-S3	cervix
25	chr1:222884200-222887200	Active TSS	NH-A	brain
26	chr1:222884200-222887400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:222884200-222887400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:222884200-222887400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:222884200-222887400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:222884200-222887400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:222884200-222887400	Active TSS	HSMMtube	muscle
32	chr1:222884200-222887600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:222884200-222887600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:222884200-222887600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:222884200-222887600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:222884200-222887600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:222884200-222887600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:222884200-222887600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:222884200-222887600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:222884200-222887600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:222884200-222887600	Active TSS	Fetal Stomach	stomach
42	chr1:222884200-222887600	Active TSS	NHDF-Ad	bronchial
43	chr1:222884200-222888000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:222884400-222887200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:222884400-222887200	Active TSS	Colon Smooth Muscle	Colon
46	chr1:222884400-222887200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:222884400-222887200	Active TSS	HUVEC	blood vessel
48	chr1:222884400-222887200	Active TSS	NHEK	skin
49	chr1:222884400-222887400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:222884400-222887400	Active TSS	Cortex derived primary cultured neurospheres	brain

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