Variant report

Variant	rs3748644
Chromosome Location	chr1:45965771-45965772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:468)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:468 , 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	SIN3AK20	chr1:45965318-45966184	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:45965432-45966292	K562	blood:	n/a	n/a
3	POLR2A	chr1:45965620-45966270	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr1:45965465-45966201	HepG2	liver:	n/a	n/a
5	YY1	chr1:45965477-45966308	K562	blood:	n/a	n/a
6	NFIC	chr1:45965443-45966278	GM12878	blood:	n/a	n/a
7	CEBPB	chr1:45965561-45966178	K562	blood:	n/a	chr1:45966124-45966132
8	RAD21	chr1:45965281-45965854	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr1:45965436-45966220	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr1:45965444-45966246	SK-N-MC	brain:	n/a	n/a
11	BATF	chr1:45965502-45966200	GM12878	blood:	n/a	n/a
12	RFX5	chr1:45965515-45966139	GM12878	blood:	n/a	n/a
13	IRF1	chr1:45965535-45966113	K562	blood:	n/a	n/a
14	YY1	chr1:45965695-45966181	GM12878	blood:	n/a	n/a
15	BCLAF1	chr1:45965465-45966215	GM12878	blood:	n/a	n/a
16	IRF4	chr1:45965536-45966325	GM12878	blood:	n/a	n/a
17	TCF7L2	chr1:45965439-45966185	PANC-1	pancreas:	n/a	n/a
18	ETS1	chr1:45965359-45966195	GM12878	blood:	n/a	n/a
19	YY1	chr1:45965543-45966127	K562	blood:	n/a	n/a
20	POLR2A	chr1:45965377-45966221	HCT-116	colon:	n/a	n/a
21	RFX5	chr1:45965364-45966201	Hela-S3	cervix:	n/a	n/a
22	SP1	chr1:45965572-45966199	A549	lung:	n/a	n/a
23	TBP	chr1:45965415-45966264	K562	blood:	n/a	n/a
24	CTCF	chr1:45965640-45965790	BE2_C	brain:	n/a	n/a
25	TAF1	chr1:45965392-45966278	ECC-1	luminal epithelium:	n/a	n/a
26	YY1	chr1:45965463-45966306	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr1:45965342-45966340	ECC-1	luminal epithelium:	n/a	n/a
28	RFX5	chr1:45965413-45966132	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:45965488-45966198	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr1:45965599-45965783	A549	lung:	n/a	n/a
31	FOXM1	chr1:45965471-45966264	GM12878	blood:	n/a	n/a
32	YY1	chr1:45965631-45966244	GM12891	blood:	n/a	n/a
33	POLR2A	chr1:45965470-45966171	GM12878	blood:	n/a	n/a
34	ZEB1	chr1:45965547-45966160	GM12878	blood:	n/a	n/a
35	CTCF	chr1:45965444-45966002	K562	blood:	n/a	n/a
36	FOXM1	chr1:45965531-45966237	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr1:45965410-45966220	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:45965325-45966325	HL-60	blood:	n/a	n/a
39	RELA	chr1:45965145-45966187	GM15510	blood:	n/a	n/a
40	YY1	chr1:45965476-45966228	SK-N-SH	brain:	n/a	n/a
41	PAX5	chr1:45965475-45966123	GM12878	blood:	n/a	n/a
42	ETS1	chr1:45965528-45966227	K562	blood:	n/a	n/a
43	ZNF143	chr1:45965225-45966236	K562	blood:	n/a	n/a
44	CEBPB	chr1:45965469-45966636	HepG2	liver:	n/a	chr1:45966124-45966132
45	PAX5	chr1:45965575-45966185	GM12878	blood:	n/a	n/a
46	YY1	chr1:45965545-45966164	K562	blood:	n/a	n/a
47	YY1	chr1:45965433-45966183	HCT-116	colon:	n/a	n/a
48	TCF12	chr1:45965518-45966261	ECC-1	luminal epithelium:	n/a	n/a
49	SIX5	chr1:45965514-45966259	GM12878	blood:	n/a	n/a
50	REST	chr1:45965144-45966351	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45965727-45965777	ECC-1	luminal epithelium:	n/a
2	chr1:45965727-45965777	ProgFib	skin:	n/a
3	chr1:45965727-45965777	PFSK-1	brain:	n/a
4	chr1:45965727-45965777	HEEpiC	esophagus:	n/a
5	chr1:45965727-45965777	AG04449	skin:	fetal
6	chr1:45965727-45965777	BJ	skin:	n/a
7	chr1:45965727-45965777	Hepatocyte	liver:	n/a
8	chr1:45965727-45965777	AG10803	skin:	n/a
9	chr1:45965727-45965777	SK-N-SH_RA	brain:	n/a
10	chr1:45965727-45965777	PANC-1	pancreas:	n/a
11	chr1:45965727-45965777	NH-A	brain:	n/a
12	chr1:45965727-45965777	BE2_C	brain:	n/a
13	chr1:45965727-45965777	ovcar-3	ovarian:	n/a
14	chr1:45965727-45965777	IMR90	lung:	fetal
15	chr1:45965727-45965777	HPAEpiC	pulmonary alveolar:	n/a
16	chr1:45965727-45965777	HUVEC	blood vessel:	n/a
17	chr1:45965727-45965777	MCF10A-Er-Src	breast:	n/a
18	chr1:45965727-45965777	GM12891	blood:	n/a
19	chr1:45965727-45965777	NB4	blood:	n/a
20	chr1:45965727-45965777	SKMC	muscle:	n/a
21	chr1:45965727-45965777	Hela-S3	cervix:	n/a
22	chr1:45965727-45965777	GM12892	blood:	n/a
23	chr1:45965727-45965777	NHDF-neo	bronchial:	n/a
24	chr1:45965727-45965777	T-47D	breast:	n/a
25	chr1:45965727-45965777	SK-N-SH	brain:	n/a
26	chr1:45965727-45965777	HepG2	liver:	n/a
27	chr1:45965727-45965777	GM19239	blood:	n/a
28	chr1:45965727-45965777	NT2-D1	testis:	n/a
29	chr1:45965727-45965777	H1-hESC	embryonic stem cell:	embryo
30	chr1:45965727-45965777	Caco-2	colon:	n/a
31	chr1:45965727-45965777	GM12878	blood:	n/a
32	chr1:45965727-45965777	NHBE	bronchial:	n/a
33	chr1:45965727-45965777	AG09319	gingival:	n/a
34	chr1:45965727-45965777	HCF	heart:	n/a
35	chr1:45965727-45965777	HAEpiC	amniotic membrane:	n/a
36	chr1:45965727-45965777	HIPEpiC	eye:	n/a
37	chr1:45965727-45965777	AoSMC	blood vessel:	n/a
38	chr1:45965727-45965777	HCPEpiC	choroid plexus:	n/a
39	chr1:45965727-45965777	HRCEpiC	kidney:	n/a
40	chr1:45965727-45965777	HMEC	breast:	n/a
41	chr1:45965727-45965777	MCF-7	breast:	n/a
42	chr1:45965727-45965777	GM06990	blood:	n/a
43	chr1:45965727-45965777	HRPEpiC	eye:	n/a
44	chr1:45965727-45965777	HCM	heart:	n/a
45	chr1:45965727-45965777	K562	blood:	n/a
46	chr1:45965727-45965777	SK-N-MC	brain:	n/a
47	chr1:45965727-45965777	HRE	kidney:	n/a
48	chr1:45965727-45965777	HNPCEpiC	eye:	n/a
49	chr1:45965727-45965777	U87	brain:	n/a
50	chr1:45965727-45965777	HEK293	kidney:	embryo

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45239737..45242586-chr1:45965500..45967251,2	K562	blood:
2	chr1:45804114..45807301-chr1:45961577..45967419,8	K562	blood:
3	chr1:45185969..45188598-chr1:45964540..45967567,4	K562	blood:
4	chr1:45283510..45287262-chr1:45964108..45968951,6	K562	blood:
5	chr1:45806085..45807923-chr1:45963911..45966246,2	MCF-7	breast:
6	chr1:45768003..45772070-chr1:45964648..45967315,5	K562	blood:
7	chr1:45963397..45969763-chr1:46047572..46053150,23	K562	blood:
8	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
9	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
10	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
11	chr1:45964150..45967582-chr1:46014583..46018871,5	K562	blood:
12	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
13	chr1:45284392..45287262-chr1:45964108..45967526,3	K562	blood:
14	chr1:45804471..45806506-chr1:45965051..45967533,2	K562	blood:
15	chr1:45965671..45969478-chr1:45972057..45975317,5	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC163P	TF binding region
CCDC163P	CpG island
ENSG00000200913	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000070759	Chromatin interaction
ENSG00000173846	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006215	1.00[JPT][hapmap]
rs1007859	0.83[ASN][1000 genomes]
rs10493120	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11211110	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11211115	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12022634	0.83[ASN][1000 genomes]
rs12032658	0.83[ASN][1000 genomes]
rs12042481	1.00[JPT][hapmap]
rs1691216	0.83[ASN][1000 genomes]
rs1691217	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1691218	0.83[ASN][1000 genomes]
rs1691221	0.83[ASN][1000 genomes]
rs1765710	0.83[ASN][1000 genomes]
rs1771549	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2065708	1.00[JPT][hapmap]
rs2642901	0.83[ASN][1000 genomes]
rs28789981	0.83[ASN][1000 genomes]
rs3748643	1.00[JPT][hapmap]
rs781057	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs781062	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs781063	0.83[ASN][1000 genomes]
rs945179	1.00[JPT][hapmap]
rs947112	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 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	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
2	chr1:45964400-45966600	Active TSS	A549	lung
3	chr1:45964400-45966800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:45964600-45966600	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:45964800-45966200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:45964800-45966600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:45964800-45966600	Active TSS	Ovary	ovary
8	chr1:45964800-45967200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:45964800-45967400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:45965000-45965800	Flanking Active TSS	HUVEC	blood vessel
11	chr1:45965000-45966200	Bivalent/Poised TSS	HepG2	liver
12	chr1:45965000-45966400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:45965000-45966600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:45965000-45966600	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:45965000-45966600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr1:45965000-45966600	Active TSS	Pancreas	Pancrea
17	chr1:45965000-45966800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:45965000-45966800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:45965000-45966800	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr1:45965000-45966800	Active TSS	Fetal Kidney	kidney
21	chr1:45965000-45966800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:45965000-45966800	Active TSS	NHLF	lung
23	chr1:45965000-45967000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:45965000-45967000	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr1:45965000-45967200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:45965000-45967200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:45965200-45966200	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr1:45965200-45966200	Active TSS	Stomach Mucosa	stomach
29	chr1:45965200-45966400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:45965200-45966400	Active TSS	Aorta	Aorta
31	chr1:45965200-45966400	Active TSS	Gastric	stomach
32	chr1:45965200-45966600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:45965200-45966600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:45965200-45966600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:45965200-45966600	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:45965200-45966600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:45965200-45966600	Active TSS	Psoas Muscle	Psoas
38	chr1:45965200-45966800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45965200-45966800	Active TSS	Fetal Intestine Large	intestine
40	chr1:45965200-45967000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr1:45965200-45967000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:45965400-45966000	Active TSS	Primary T cells from cord blood	blood
43	chr1:45965400-45966000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:45965400-45966000	Active TSS	Fetal Thymus	thymus
45	chr1:45965400-45966000	Active TSS	Thymus	Thymus
46	chr1:45965400-45966000	Active TSS	Dnd41	blood
47	chr1:45965400-45966200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:45965400-45966400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:45965400-45966400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr1:45965400-45966400	Active TSS	Fetal Heart	heart

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