Variant report

Variant	rs3738035
Chromosome Location	chr1:225965527-225965528
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:514)
CpG islands
(count:61)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:514 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:225965150-225966189	Hela-S3	cervix:	n/a	n/a
2	REST	chr1:225965161-225966221	H1-neurons	neurons:	n/a	chr1:225965437-225965450 chr1:225966018-225966031
3	TAF1	chr1:225965232-225966135	GM12892	blood:	n/a	n/a
4	TBP	chr1:225964946-225966540	K562	blood:	n/a	n/a
5	FOXA2	chr1:225964779-225965641	A549	lung:	n/a	n/a
6	E2F6	chr1:225965264-225965547	K562	blood:	n/a	n/a
7	MYC	chr1:225965252-225966238	MCF10A-Er-Src	breast:	n/a	n/a
8	REST	chr1:225964745-225966624	H1-neurons	neurons:	n/a	chr1:225965437-225965450 chr1:225966018-225966031
9	POLR2A	chr1:225964963-225966193	K562	blood:	n/a	n/a
10	EGR1	chr1:225965239-225965544	H1-hESC	embryonic stem cell:	n/a	chr1:225965440-225965451 chr1:225965439-225965452 chr1:225965438-225965452 chr1:225965438-225965453
11	MAX	chr1:225964765-225966170	K562	blood:	n/a	n/a
12	PAX5	chr1:225965080-225965636	GM12891	blood:	n/a	n/a
13	GATA3	chr1:225965117-225965617	T-47D	breast:	n/a	n/a
14	IRF1	chr1:225965137-225966091	K562	blood:	n/a	chr1:225965434-225965448
15	YY1	chr1:225965143-225966122	HCT-116	colon:	n/a	chr1:225965436-225965450 chr1:225965528-225965538 chr1:225965528-225965550 chr1:225965531-225965539 chr1:225965526-225965545 chr1:225965529-225965537
16	MAX	chr1:225965114-225965616	SK-N-SH	brain:	n/a	n/a
17	MAX	chr1:225964778-225966336	A549	lung:	n/a	n/a
18	YY1	chr1:225965166-225966184	GM12878	blood:	n/a	chr1:225965436-225965450 chr1:225965528-225965538 chr1:225965528-225965550 chr1:225965531-225965539 chr1:225965526-225965545 chr1:225965529-225965537
19	CTCF	chr1:225965192-225965545	ECC-1	luminal epithelium:	n/a	chr1:225965527-225965545
20	ELF1	chr1:225964860-225966212	GM12878	blood:	n/a	n/a
21	PML	chr1:225965118-225966158	MCF-7	breast:	n/a	n/a
22	EP300	chr1:225965298-225965994	HepG2	liver:	n/a	chr1:225965441-225965454
23	SP1	chr1:225965009-225966031	A549	lung:	n/a	chr1:225965459-225965480 chr1:225966017-225966029 chr1:225965436-225965448 chr1:225965437-225965451 chr1:225966017-225966029 chr1:225965436-225965448
24	JUND	chr1:225965190-225965699	HepG2	liver:	n/a	n/a
25	RAD21	chr1:225965048-225965619	ECC-1	luminal epithelium:	n/a	chr1:225965527-225965539
26	JUND	chr1:225965054-225966108	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:225965070-225966087	HCT-116	colon:	n/a	n/a
28	MEF2A	chr1:225965236-225965631	GM12878	blood:	n/a	n/a
29	SMARCB1	chr1:225964815-225966047	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:225965057-225966493	HepG2	liver:	n/a	n/a
31	TBP	chr1:225965221-225966467	GM12878	blood:	n/a	n/a
32	ZC3H11A	chr1:225965128-225966163	K562	blood:	n/a	n/a
33	MYC	chr1:225965207-225965712	MCF-7	breast:	n/a	n/a
34	RAD21	chr1:225965084-225965718	MCF-7	breast:	n/a	chr1:225965527-225965539
35	MAX	chr1:225965221-225966133	H1-hESC	embryonic stem cell:	n/a	n/a
36	CEBPB	chr1:225965169-225966176	K562	blood:	n/a	n/a
37	CTCF	chr1:225965177-225965528	T-47D	breast:	n/a	n/a
38	HDAC2	chr1:225965128-225965561	K562	blood:	n/a	n/a
39	MAX	chr1:225965162-225966241	ECC-1	luminal epithelium:	n/a	n/a
40	YY1	chr1:225964787-225966183	GM12891	blood:	n/a	chr1:225965436-225965450 chr1:225965528-225965538 chr1:225965528-225965550 chr1:225965531-225965539 chr1:225965526-225965545 chr1:225965529-225965537
41	POLR2A	chr1:225964866-225966169	K562	blood:	n/a	n/a
42	TCF7L2	chr1:225965186-225966093	HCT-116	colon:	n/a	n/a
43	SIN3A	chr1:225965142-225966115	GM12878	blood:	n/a	n/a
44	CHD2	chr1:225965068-225966071	HepG2	liver:	n/a	n/a
45	ZNF143	chr1:225965136-225966064	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr1:225965056-225966246	A549	lung:	n/a	n/a
47	CTCF	chr1:225965161-225965530	HepG2	liver:	n/a	n/a
48	SMC3	chr1:225965060-225966233	Hela-S3	cervix:	n/a	n/a
49	CBX3	chr1:225965105-225965602	K562	blood:	n/a	n/a
50	SIN3AK20	chr1:225964752-225966281	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:225965511-225965561	NHBE	bronchial:	n/a
2	chr1:225965511-225965561	GM19239	blood:	n/a
3	chr1:225965511-225965561	HRE	kidney:	n/a
4	chr1:225965511-225965561	SKMC	muscle:	n/a
5	chr1:225965511-225965561	SK-N-MC	brain:	n/a
6	chr1:225965511-225965561	AG09319	gingival:	n/a
7	chr1:225965511-225965561	HNPCEpiC	eye:	n/a
8	chr1:225965511-225965561	ProgFib	skin:	n/a
9	chr1:225965511-225965561	Caco-2	colon:	n/a
10	chr1:225965511-225965561	K562	blood:	n/a
11	chr1:225965511-225965561	PFSK-1	brain:	n/a
12	chr1:225965511-225965561	CMK	blood:	n/a
13	chr1:225965511-225965561	HEK293	kidney:	embryo
14	chr1:225965511-225965561	H1-hESC	embryonic stem cell:	embryo
15	chr1:225965511-225965561	BE2_C	brain:	n/a
16	chr1:225965511-225965561	AG10803	skin:	n/a
17	chr1:225965511-225965561	A549	lung:	n/a
18	chr1:225965511-225965561	HepG2	liver:	n/a
19	chr1:225965511-225965561	HRPEpiC	eye:	n/a
20	chr1:225965511-225965561	NB4	blood:	n/a
21	chr1:225965511-225965561	HCT-116	colon:	n/a
22	chr1:225965511-225965561	Hela-S3	cervix:	n/a
23	chr1:225965511-225965561	MCF10A-Er-Src	breast:	n/a
24	chr1:225965511-225965561	PANC-1	pancreas:	n/a
25	chr1:225965511-225965561	SK-N-SH_RA	brain:	n/a
26	chr1:225965511-225965561	BJ	skin:	n/a
27	chr1:225965511-225965561	HAEpiC	amniotic membrane:	n/a
28	chr1:225965511-225965561	Jurkat	blood:	n/a
29	chr1:225965511-225965561	NT2-D1	testis:	n/a
30	chr1:225965511-225965561	PrEC	prostate:	n/a
31	chr1:225965511-225965561	IMR90	lung:	fetal
32	chr1:225965511-225965561	GM12892	blood:	n/a
33	chr1:225965511-225965561	ovcar-3	ovarian:	n/a
34	chr1:225965511-225965561	RPTEC	kidney:	n/a
35	chr1:225965511-225965561	HCPEpiC	choroid plexus:	n/a
36	chr1:225965511-225965561	AG04449	skin:	fetal
37	chr1:225965511-225965561	GM12878	blood:	n/a
38	chr1:225965511-225965561	SK-N-SH	brain:	n/a
39	chr1:225965511-225965561	ECC-1	luminal epithelium:	n/a
40	chr1:225965511-225965561	SAEC	small airway:	n/a
41	chr1:225965511-225965561	HL-60	blood:	n/a
42	chr1:225965511-225965561	HUVEC	blood vessel:	n/a
43	chr1:225965511-225965561	LNCaP	prostate:	n/a
44	chr1:225965511-225965561	NH-A	brain:	n/a
45	chr1:225965511-225965561	HMEC	breast:	n/a
46	chr1:225965511-225965561	MCF-7	breast:	n/a
47	chr1:225965511-225965561	T-47D	breast:	n/a
48	chr1:225965511-225965561	HEEpiC	esophagus:	n/a
49	chr1:225965511-225965561	NHDF-neo	bronchial:	n/a
50	chr1:225965511-225965561	HRCEpiC	kidney:	n/a

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:225965395..225967471-chr12:117490550..117492773,2	MCF-7	breast:
2	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:
3	chr1:28832123..28832938-chr1:225965487..225966037,2	Hela-S3	cervix:
4	chr1:225965483..225966004-chr15:67813277..67813999,2	Hela-S3	cervix:
5	chr1:225965438..225966023-chr5:148650836..148651793,2	Hela-S3	cervix:
6	chr1:225837738..225841787-chr1:225965241..225967265,3	MCF-7	breast:
7	chr1:225964211..225968767-chr1:226248453..226252378,4	K562	blood:
8	chr1:225964614..225966521-chr1:226248789..226250672,2	K562	blood:
9	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
10	chr1:225652849..225654996-chr1:225964946..225967311,2	MCF-7	breast:
11	chr1:225963541..225967644-chr1:226069236..226073918,5	MCF-7	breast:
12	chr1:225963873..225967033-chr1:226031330..226035962,4	MCF-7	breast:
13	chr1:225963989..225965773-chr1:226185779..226187510,2	K562	blood:
14	chr1:225964871..225966516-chr1:226110750..226112942,2	MCF-7	breast:
15	chr1:225964533..225968744-chr1:226068261..226071590,3	MCF-7	breast:
16	chr1:225686982..225689320-chr1:225964805..225966549,2	MCF-7	breast:
17	chr1:225963779..225965569-chr1:226150173..226152058,2	MCF-7	breast:
18	chr1:225964273..225967291-chr1:226184778..226188048,4	K562	blood:
19	chr1:225963673..225968224-chr1:226032543..226034938,4	MCF-7	breast:
20	chr1:225965401..225967311-chr1:226185341..226187298,3	MCF-7	breast:
21	chr1:225965429..225965968-chr17:74705524..74706086,2	NB4	blood:
22	chr1:225963904..225970275-chr1:225994893..226001084,15	K562	blood:
23	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
24	chr1:225698646..225701113-chr1:225965307..225966901,2	MCF-7	breast:
25	chr1:225964257..225969087-chr1:226030786..226035881,7	K562	blood:
26	chr1:225965472..225966023-chr15:72978001..72978969,2	Hela-S3	cervix:
27	chr1:225965000..225971731-chr1:226051573..226055609,6	K562	blood:
28	chr1:225962294..225967531-chr1:225994011..226002080,11	K562	blood:
29	chr1:225965466..225966431-chr12:49658590..49659116,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SRP9	TF binding region
SRP9	CpG island
ENSG00000167553	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000182534	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000175202	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000157510	Chromatin interaction
ENSG00000154380	Chromatin interaction
ENSG00000213032	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143819	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000088992	Chromatin interaction
ENSG00000259673	Chromatin interaction
ENSG00000189227	Chromatin interaction
ENSG00000140463	Chromatin interaction
ENSG00000242861	Chromatin interaction
ENSG00000234476	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000242125	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10915869	1.00[AFR][1000 genomes]
rs10915871	1.00[AFR][1000 genomes]
rs10915872	1.00[AFR][1000 genomes]
rs10915874	1.00[AFR][1000 genomes]
rs10915875	1.00[AFR][1000 genomes]
rs11583055	0.87[CEU][hapmap]
rs12021669	1.00[AFR][1000 genomes]
rs12021809	1.00[AFR][1000 genomes]
rs12023203	1.00[AFR][1000 genomes]
rs12025075	1.00[AFR][1000 genomes]
rs12025085	1.00[AFR][1000 genomes]
rs12025267	1.00[AFR][1000 genomes]
rs12026657	1.00[AFR][1000 genomes]
rs12029847	1.00[AFR][1000 genomes]
rs12031637	1.00[AFR][1000 genomes]
rs12032511	1.00[AFR][1000 genomes]
rs12034342	1.00[AFR][1000 genomes]
rs12038476	1.00[AFR][1000 genomes]
rs12039184	1.00[AFR][1000 genomes]
rs12047520	1.00[AFR][1000 genomes]
rs12048908	1.00[AFR][1000 genomes]
rs12562612	1.00[AFR][1000 genomes]
rs1849685	1.00[AFR][1000 genomes]
rs2078389	1.00[AFR][1000 genomes]
rs3753650	1.00[AFR][1000 genomes]
rs3753658	0.80[CHB][hapmap]
rs4557929	1.00[AFR][1000 genomes]
rs56187333	0.82[EUR][1000 genomes]
rs61849043	1.00[AFR][1000 genomes]
rs61849046	1.00[AFR][1000 genomes]
rs61849047	1.00[AFR][1000 genomes]
rs61851667	1.00[AFR][1000 genomes]
rs716966	1.00[AFR][1000 genomes]

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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 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	chr1:225952200-225965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:225964400-225966400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:225964400-225966600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:225964400-225966800	Active TSS	NHDF-Ad	bronchial
5	chr1:225964600-225965800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:225964600-225966200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:225964600-225966400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:225964600-225966600	Active TSS	Brain Hippocampus Middle	brain
9	chr1:225964600-225966800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:225964600-225967000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:225964600-225967000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:225964600-225967000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:225964600-225967000	Active TSS	Right Ventricle	heart
14	chr1:225964600-225967200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:225964600-225967400	Active TSS	A549	lung
16	chr1:225964800-225965600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:225964800-225966000	Bivalent/Poised TSS	HepG2	liver
18	chr1:225964800-225966200	Active TSS	Brain Substantia Nigra	brain
19	chr1:225964800-225966200	Active TSS	Colonic Mucosa	Colon
20	chr1:225964800-225966200	Active TSS	Esophagus	oesophagus
21	chr1:225964800-225966200	Active TSS	Lung	lung
22	chr1:225964800-225966800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:225964800-225966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:225964800-225966800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr1:225964800-225967000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:225964800-225967000	Active TSS	Aorta	Aorta
27	chr1:225964800-225967000	Active TSS	Left Ventricle	heart
28	chr1:225964800-225967000	Active TSS	HSMMtube	muscle
29	chr1:225964800-225967200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:225964800-225967200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:225964800-225967200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:225964800-225967200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:225964800-225967200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:225964800-225967200	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr1:225964800-225967200	Active TSS	Fetal Kidney	kidney
36	chr1:225964800-225967200	Active TSS	Ovary	ovary
37	chr1:225965000-225965600	Weak transcription	Spleen	Spleen
38	chr1:225965000-225966200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr1:225965000-225966200	Active TSS	Gastric	stomach
40	chr1:225965000-225966400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr1:225965000-225966400	Active TSS	Rectal Smooth Muscle	rectum
42	chr1:225965000-225966600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:225965000-225966600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:225965000-225966600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:225965000-225966600	Active TSS	Fetal Brain Female	brain
46	chr1:225965000-225966600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr1:225965000-225966800	Active TSS	Psoas Muscle	Psoas
48	chr1:225965000-225967000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:225965000-225967000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:225965000-225967000	Active TSS	Fetal Intestine Large	intestine

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