Variant report

Variant	rs17531007
Chromosome Location	chr1:222817799-222817800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:454)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:454 , 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	REST	chr1:222817091-222817843	K562	blood:	n/a	n/a
2	GABPA	chr1:222817119-222817890	A549	lung:	n/a	n/a
3	POLR2A	chr1:222817026-222818199	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr1:222817105-222817856	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr1:222816715-222818171	K562	blood:	n/a	chr1:222817584-222817594
6	EP300	chr1:222817071-222818141	GM12878	blood:	n/a	chr1:222817587-222817603 chr1:222817128-222817142
7	EP300	chr1:222817256-222817828	GM12878	blood:	n/a	chr1:222817587-222817603
8	POLR2A	chr1:222817176-222817965	HepG2	liver:	n/a	n/a
9	SP1	chr1:222817222-222817854	K562	blood:	n/a	chr1:222817583-222817595 chr1:222817584-222817594 chr1:222817583-222817594 chr1:222817584-222817593 chr1:222817585-222817594 chr1:222817583-222817595
10	POLR2A	chr1:222816609-222818170	GM19099	blood:	n/a	n/a
11	MAX	chr1:222817059-222817970	ECC-1	luminal epithelium:	n/a	chr1:222817584-222817594
12	POLR2A	chr1:222816540-222818422	GM12891	blood:	n/a	n/a
13	ELF1	chr1:222817028-222818031	HepG2	liver:	n/a	chr1:222817495-222817504
14	POLR2A	chr1:222816935-222818113	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:222816709-222818099	Raji	blood:	n/a	n/a
16	FOXP2	chr1:222817388-222817848	SK-N-MC	brain:	n/a	n/a
17	HNF4A	chr1:222817420-222817868	HepG2	liver:	n/a	n/a
18	E2F4	chr1:222817364-222818006	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:222816980-222818044	ProgFib	skin:	n/a	n/a
20	POLR2A	chr1:222817217-222817980	HepG2	liver:	n/a	n/a
21	MAX	chr1:222817008-222818195	NB4	blood:	n/a	chr1:222817584-222817594
22	ELF1	chr1:222816908-222818082	A549	lung:	n/a	chr1:222817495-222817504
23	CREB1	chr1:222817251-222817978	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr1:222816871-222818191	GM12891	blood:	n/a	n/a
25	CHD1	chr1:222816189-222818471	IMR90	lung:	n/a	n/a
26	ELK4	chr1:222817141-222817935	Hela-S3	cervix:	n/a	chr1:222817492-222817503
27	TAF1	chr1:222816885-222818061	ECC-1	luminal epithelium:	n/a	n/a
28	ETS1	chr1:222817156-222818052	K562	blood:	n/a	chr1:222817491-222817506 chr1:222817492-222817502 chr1:222817349-222817363 chr1:222817494-222817503
29	EP300	chr1:222817298-222817843	T-47D	breast:	n/a	chr1:222817587-222817603
30	POLR2A	chr1:222816893-222817881	HCT-116	colon:	n/a	n/a
31	POLR2A	chr1:222816650-222818359	K562	blood:	n/a	n/a
32	HEY1	chr1:222817172-222818052	HepG2	liver:	n/a	chr1:222817584-222817599
33	TBL1XR1	chr1:222817062-222817973	GM12878	blood:	n/a	n/a
34	EP300	chr1:222817376-222817824	HepG2	liver:	n/a	chr1:222817587-222817603
35	MYC	chr1:222817356-222817824	HepG2	liver:	n/a	chr1:222817584-222817594
36	IRF1	chr1:222816739-222818173	K562	blood:	n/a	chr1:222817659-222817680 chr1:222817581-222817595
37	MXI1	chr1:222816860-222818102	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr1:222817331-222818083	HepG2	liver:	n/a	n/a
39	TAF1	chr1:222816967-222817853	A549	lung:	n/a	n/a
40	HMGN3	chr1:222817132-222817915	K562	blood:	n/a	n/a
41	CREB1	chr1:222816976-222818316	K562	blood:	n/a	n/a
42	CUX1	chr1:222817168-222817900	K562	blood:	n/a	n/a
43	FOSL2	chr1:222817044-222817869	A549	lung:	n/a	n/a
44	TAF1	chr1:222816957-222817893	K562	blood:	n/a	n/a
45	PBX3	chr1:222817280-222817924	SK-N-SH	brain:	n/a	chr1:222817477-222817497
46	POLR2A	chr1:222816702-222818315	GM12892	blood:	n/a	n/a
47	SIN3AK20	chr1:222817089-222818128	A549	lung:	n/a	n/a
48	POLR2A	chr1:222817134-222817864	SK-N-SH	brain:	n/a	n/a
49	SMARCB1	chr1:222817037-222818053	Hela-S3	cervix:	n/a	n/a
50	ATF3	chr1:222817448-222817814	H1-hESC	embryonic stem cell:	n/a	chr1:222817632-222817652

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:222817780-222817830	SAEC	small airway:	n/a
2	chr1:222817780-222817830	HepG2	liver:	n/a
3	chr1:222817780-222817830	HMEC	breast:	n/a
4	chr1:222817780-222817830	HIPEpiC	eye:	n/a
5	chr1:222817780-222817830	HAEpiC	amniotic membrane:	n/a
6	chr1:222817780-222817830	Jurkat	blood:	n/a
7	chr1:222817780-222817830	LNCaP	prostate:	n/a
8	chr1:222817780-222817830	HRPEpiC	eye:	n/a
9	chr1:222817780-222817830	HNPCEpiC	eye:	n/a
10	chr1:222817780-222817830	HPAEpiC	pulmonary alveolar:	n/a
11	chr1:222817780-222817830	MCF10A-Er-Src	breast:	n/a
12	chr1:222817780-222817830	U87	brain:	n/a
13	chr1:222817780-222817830	Hela-S3	cervix:	n/a
14	chr1:222817780-222817830	HEK293	kidney:	embryo
15	chr1:222817780-222817830	SK-N-MC	brain:	n/a
16	chr1:222817780-222817830	PFSK-1	brain:	n/a
17	chr1:222817780-222817830	SK-N-SH_RA	brain:	n/a
18	chr1:222817780-222817830	AG04450	lung:	fetal
19	chr1:222817780-222817830	AG09309	skin:	n/a
20	chr1:222817780-222817830	HCF	heart:	n/a
21	chr1:222817780-222817830	AG09319	gingival:	n/a
22	chr1:222817780-222817830	MCF-7	breast:	n/a
23	chr1:222817780-222817830	CMK	blood:	n/a
24	chr1:222817780-222817830	NHDF-neo	bronchial:	n/a
25	chr1:222817780-222817830	HRE	kidney:	n/a
26	chr1:222817780-222817830	HL-60	blood:	n/a
27	chr1:222817780-222817830	GM19239	blood:	n/a
28	chr1:222817780-222817830	SK-N-SH	brain:	n/a
29	chr1:222817780-222817830	HUVEC	blood vessel:	n/a
30	chr1:222817780-222817830	GM06990	blood:	n/a
31	chr1:222817780-222817830	NHBE	bronchial:	n/a
32	chr1:222817780-222817830	NH-A	brain:	n/a
33	chr1:222817780-222817830	T-47D	breast:	n/a
34	chr1:222817780-222817830	Hepatocyte	liver:	n/a
35	chr1:222817780-222817830	HCT-116	colon:	n/a
36	chr1:222817780-222817830	A549	lung:	n/a
37	chr1:222817780-222817830	K562	blood:	n/a
38	chr1:222817780-222817830	AoSMC	blood vessel:	n/a
39	chr1:222817780-222817830	AG04449	skin:	fetal
40	chr1:222817780-222817830	NB4	blood:	n/a
41	chr1:222817780-222817830	BE2_C	brain:	n/a
42	chr1:222817780-222817830	NT2-D1	testis:	n/a
43	chr1:222817780-222817830	ECC-1	luminal epithelium:	n/a
44	chr1:222817780-222817830	GM12892	blood:	n/a
45	chr1:222817780-222817830	IMR90	lung:	fetal
46	chr1:222817780-222817830	HEEpiC	esophagus:	n/a
47	chr1:222817780-222817830	HCPEpiC	choroid plexus:	n/a
48	chr1:222817780-222817830	GM12878	blood:	n/a
49	chr1:222817780-222817830	BJ	skin:	n/a
50	chr1:222817780-222817830	RPTEC	kidney:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:222814795..222819438-chr1:222884035..222887873,13	K562	blood:
2	chr1:222761198..222763394-chr1:222816241..222819069,2	K562	blood:
3	chr1:222789107..222793717-chr1:222814287..222819011,10	K562	blood:
4	chr1:222790877..222794262-chr1:222817668..222820285,3	MCF-7	breast:
5	chr1:222816933..222819100-chr1:222834674..222837406,2	K562	blood:
6	chr1:222816758..222818499-chr1:222830262..222833002,2	K562	blood:
7	chr1:222815720..222818727-chr1:222847963..222850560,3	K562	blood:
8	chr1:222815622..222820703-chr1:222883498..222888165,14	K562	blood:
9	chr1:222560163..222562187-chr1:222816879..222819100,2	K562	blood:
10	chr1:222817680..222819791-chr1:222885041..222887043,2	MCF-7	breast:
11	chr1:222817247..222819039-chr1:222835684..222838634,2	MCF-7	breast:
12	chr1:222788934..222792471-chr1:222815936..222819007,5	MCF-7	breast:
13	chr1:222788058..222793799-chr1:222815102..222819462,10	K562	blood:
14	chr1:222816842..222820047-chr1:222820781..222823646,5	K562	blood:
15	chr1:222817285..222820043-chr1:222820783..222823555,3	K562	blood:
16	chr1:222762024..222764722-chr1:222816738..222818394,2	MCF-7	breast:
17	chr1:222762853..222764726-chr1:222816205..222818798,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MIA3-1	chr1:222817657-222817804	ENSG00000244697.1

No data

Variant related genes	Relation type
MIA3	TF binding region
ENSG00000229399	TF binding region
ENSG00000229399	CpG island
MIA3	CpG island
ENSG00000236230	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000143498	Chromatin interaction
ENSG00000162819	Chromatin interaction
ENSG00000225265	Chromatin interaction
ENSG00000272750	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17163490	1.00[ASN][1000 genomes]
rs17474354	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17531580	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532981	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2378605	1.00[CHB][hapmap]
rs3002145	1.00[CHB][hapmap]
rs4240934	1.00[CHB][hapmap]
rs74145503	1.00[ASN][1000 genomes]
rs904323	1.00[CHB][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222816600-222818000	Active TSS	Brain Angular Gyrus	brain
2	chr1:222816600-222818000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:222816600-222818400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:222816600-222818400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr1:222816600-222818400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:222816600-222818400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:222816600-222818400	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:222816600-222818600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:222816600-222818600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:222816600-222818600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:222816800-222817800	Active TSS	Brain Substantia Nigra	brain
12	chr1:222816800-222818000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:222816800-222818000	Active TSS	Fetal Muscle Leg	muscle
14	chr1:222816800-222818200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:222816800-222818200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:222816800-222818200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:222816800-222818200	Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr1:222816800-222818200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:222816800-222818200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:222816800-222818200	Active TSS	Brain Anterior Caudate	brain
21	chr1:222816800-222818200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:222816800-222818200	Active TSS	Duodenum Mucosa	Duodenum
23	chr1:222816800-222818200	Active TSS	Fetal Brain Female	brain
24	chr1:222816800-222818200	Active TSS	Placenta	Placenta
25	chr1:222816800-222818200	Active TSS	HSMM	muscle
26	chr1:222816800-222818200	Active TSS	NH-A	brain
27	chr1:222816800-222818200	Active TSS	NHDF-Ad	bronchial
28	chr1:222816800-222818400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:222816800-222818400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:222816800-222818400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:222816800-222818400	Active TSS	Colonic Mucosa	Colon
32	chr1:222816800-222818400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:222816800-222818400	Active TSS	Fetal Kidney	kidney
34	chr1:222816800-222818400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr1:222816800-222818400	Active TSS	Left Ventricle	heart
36	chr1:222816800-222818400	Active TSS	Psoas Muscle	Psoas
37	chr1:222816800-222818400	Active TSS	Right Atrium	heart
38	chr1:222816800-222818400	Active TSS	Right Ventricle	heart
39	chr1:222816800-222818400	Active TSS	A549	lung
40	chr1:222816800-222818400	Active TSS	GM12878-XiMat	blood
41	chr1:222816800-222818600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:222816800-222818600	Active TSS	Fetal Intestine Large	intestine
43	chr1:222816800-222818600	Active TSS	Thymus	Thymus
44	chr1:222816800-222818600	Active TSS	HSMMtube	muscle
45	chr1:222816800-222818600	Active TSS	K562	blood
46	chr1:222816800-222818800	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:222816800-222818800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:222816800-222818800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:222816800-222818800	Active TSS	NHLF	lung
50	chr1:222817000-222818000	Active TSS	Brain Cingulate Gyrus	brain

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