Variant report

Variant	rs3748545
Chromosome Location	chr1:151259543-151259544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151259288-151263774	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:151259460-151260142	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr1:151259371-151259677	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:151259214-151260075	GM12891	blood:	n/a	n/a
5	POLR2A	chr1:151258565-151268148	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:151259387-151259551	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:151259037-151266673	K562	blood:	n/a	n/a
8	POLR2A	chr1:151259317-151259601	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:151258729-151266837	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:151259107-151267227	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:151259446-151260978	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:151258969-151260451	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:151259448-151259554	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:151258710-151264070	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:151259480-151264119	HL-60	blood:	n/a	n/a
16	POLR2A	chr1:151259433-151264187	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:151258893-151264128	GM12891	blood:	n/a	n/a
18	POLR2A	chr1:151258785-151264194	K562	blood:	n/a	n/a
19	POLR2A	chr1:151258999-151264207	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:151259435-151264128	GM19193	blood:	n/a	n/a
21	POLR2A	chr1:151259084-151264063	A549	lung:	n/a	n/a
22	POLR2A	chr1:151259317-151263769	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:151259192-151259575	K562	blood:	n/a	n/a
24	POLR2A	chr1:151259533-151259995	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:151259077-151268200	K562	blood:	n/a	n/a
26	POLR2A	chr1:151258842-151264110	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:151259275-151259580	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:151259381-151259553	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:151259441-151264179	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:151259185-151261146	K562	blood:	n/a	n/a
31	POLR2A	chr1:151258964-151264093	GM12891	blood:	n/a	n/a
32	POLR2A	chr1:151259361-151266031	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:151259266-151264087	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:151259330-151260518	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:151259387-151259753	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr1:151259489-151260434	K562	blood:	n/a	n/a
37	POLR2A	chr1:151259090-151266317	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr1:151258294-151264100	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:151259411-151259549	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151259504-151259554	H1-hESC	embryonic stem cell:	embryo
2	chr1:151259504-151259554	HEEpiC	esophagus:	n/a
3	chr1:151259504-151259554	HRE	kidney:	n/a
4	chr1:151259504-151259554	HCM	heart:	n/a
5	chr1:151259504-151259554	ECC-1	luminal epithelium:	n/a
6	chr1:151259504-151259554	NT2-D1	testis:	n/a
7	chr1:151259504-151259554	BE2_C	brain:	n/a
8	chr1:151259504-151259554	MCF10A-Er-Src	breast:	n/a
9	chr1:151259504-151259554	NH-A	brain:	n/a
10	chr1:151259504-151259554	ovcar-3	ovarian:	n/a
11	chr1:151259504-151259554	LNCaP	prostate:	n/a
12	chr1:151259504-151259554	U87	brain:	n/a
13	chr1:151259504-151259554	NHDF-neo	bronchial:	n/a
14	chr1:151259504-151259554	AG09319	gingival:	n/a
15	chr1:151259504-151259554	HPAEpiC	pulmonary alveolar:	n/a
16	chr1:151259504-151259554	PFSK-1	brain:	n/a
17	chr1:151259504-151259554	GM06990	blood:	n/a
18	chr1:151259504-151259554	Jurkat	blood:	n/a
19	chr1:151259504-151259554	SK-N-SH_RA	brain:	n/a
20	chr1:151259504-151259554	GM12892	blood:	n/a
21	chr1:151259504-151259554	T-47D	breast:	n/a
22	chr1:151259504-151259554	HEK293	kidney:	embryo
23	chr1:151259504-151259554	HNPCEpiC	eye:	n/a
24	chr1:151259504-151259554	HUVEC	blood vessel:	n/a
25	chr1:151259504-151259554	AG04450	lung:	fetal
26	chr1:151259504-151259554	SK-N-SH	brain:	n/a
27	chr1:151259504-151259554	HCT-116	colon:	n/a
28	chr1:151259504-151259554	GM19239	blood:	n/a
29	chr1:151259504-151259554	HIPEpiC	eye:	n/a
30	chr1:151259504-151259554	Hela-S3	cervix:	n/a
31	chr1:151259504-151259554	Hepatocyte	liver:	n/a
32	chr1:151259504-151259554	GM12891	blood:	n/a
33	chr1:151259504-151259554	HRPEpiC	eye:	n/a
34	chr1:151259504-151259554	HRCEpiC	kidney:	n/a
35	chr1:151259504-151259554	MCF-7	breast:	n/a
36	chr1:151259504-151259554	BJ	skin:	n/a
37	chr1:151259504-151259554	PANC-1	pancreas:	n/a
38	chr1:151259504-151259554	AG10803	skin:	n/a
39	chr1:151259504-151259554	ProgFib	skin:	n/a
40	chr1:151259504-151259554	AG04449	skin:	fetal
41	chr1:151259504-151259554	HAEpiC	amniotic membrane:	n/a
42	chr1:151259504-151259554	A549	lung:	n/a
43	chr1:151259504-151259554	NB4	blood:	n/a
44	chr1:151259504-151259554	IMR90	lung:	fetal
45	chr1:151259504-151259554	HMEC	breast:	n/a
46	chr1:151259504-151259554	SKMC	muscle:	n/a
47	chr1:151259504-151259554	HCPEpiC	choroid plexus:	n/a
48	chr1:151259504-151259554	CMK	blood:	n/a
49	chr1:151259504-151259554	NHBE	bronchial:	n/a
50	chr1:151259504-151259554	GM12878	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151258574..151260250-chr1:151316879..151319085,2	MCF-7	breast:
2	1:151254384-151268403..1:151402394-151411623	GM12878	blood:
3	1:151171193-151178589..1:151254384-151268403	Hela-S3	cervix:
4	chr1:151226153..151228488-chr1:151257371..151260075,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF687	TF binding region
ZNF687	CpG island
ENSG00000143390	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000238711	Chromatin interaction
ENSG00000143398	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11204782	1.00[CHB][hapmap]
rs11577302	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11807526	0.85[CHB][hapmap]
rs12087892	0.85[CHB][hapmap]
rs12739070	0.90[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12739135	0.88[EUR][1000 genomes]
rs12743210	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1621016	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16833107	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16865250	0.85[ASN][1000 genomes]
rs1752382	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1752388	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1780586	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1972348	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298265	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2769275	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35118469	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs35485741	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35507974	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35778855	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35946639	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59912932	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523731	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
4	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151256000-151261000	Weak transcription	Fetal Kidney	kidney
2	chr1:151256000-151270600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151256800-151261600	Weak transcription	Psoas Muscle	Psoas
4	chr1:151256800-151264600	Weak transcription	NHDF-Ad	bronchial
5	chr1:151256800-151268400	Strong transcription	NHEK	skin
6	chr1:151256800-151281400	Strong transcription	Fetal Stomach	stomach
7	chr1:151257000-151259600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:151257000-151259600	Strong transcription	Thymus	Thymus
9	chr1:151257000-151260600	Weak transcription	Stomach Mucosa	stomach
10	chr1:151257000-151261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:151257000-151266400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:151257000-151266600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:151257000-151266600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:151257000-151267000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:151257000-151281200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:151257000-151281800	Weak transcription	Right Atrium	heart
17	chr1:151257200-151259800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:151257200-151261800	Genic enhancers	Pancreas	Pancrea
19	chr1:151257200-151262800	Strong transcription	K562	blood
20	chr1:151257200-151266000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:151257200-151266400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:151257200-151270200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:151257200-151283000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:151257200-151297600	Strong transcription	Dnd41	blood
25	chr1:151257400-151260200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:151257400-151261400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:151257400-151261400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr1:151257400-151261600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:151257400-151261800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:151257400-151261800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:151257400-151262200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:151257400-151263200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:151257400-151264000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:151257400-151265000	Strong transcription	Fetal Thymus	thymus
35	chr1:151257400-151265800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:151257400-151266400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:151257400-151266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:151257400-151267400	Weak transcription	Fetal Brain Male	brain
39	chr1:151257400-151272200	Strong transcription	HepG2	liver
40	chr1:151257400-151281200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:151257400-151281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:151257400-151281800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:151257400-151282000	Strong transcription	Fetal Lung	lung
44	chr1:151257400-151282200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:151257400-151282200	Strong transcription	Osteobl	bone
46	chr1:151257400-151283600	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:151257600-151259800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:151257600-151260800	Strong transcription	Spleen	Spleen
49	chr1:151257600-151261200	Strong transcription	Placenta	Placenta
50	chr1:151257600-151261400	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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