Variant report

Variant	rs2494248
Chromosome Location	chr1:47644902-47644903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:449)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:449 , 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	TBP	chr1:47644776-47645289	Hela-S3	cervix:	n/a	n/a
2	ATF3	chr1:47644723-47645070	H1-hESC	embryonic stem cell:	n/a	n/a
3	ATF3	chr1:47644679-47645155	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:47644707-47645164	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr1:47644779-47645204	HepG2	liver:	n/a	n/a
6	TAF1	chr1:47644804-47645094	GM12891	blood:	n/a	n/a
7	MYC	chr1:47644878-47645009	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:47644718-47645244	GM12891	blood:	n/a	n/a
9	HEY1	chr1:47644646-47645069	K562	blood:	n/a	n/a
10	MXI1	chr1:47644793-47645179	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:47644671-47645199	K562	blood:	n/a	n/a
12	CTCF	chr1:47644833-47645144	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr1:47644754-47644994	A549	lung:	n/a	n/a
14	POLR2A	chr1:47644768-47645044	A549	lung:	n/a	n/a
15	POLR2A	chr1:47644685-47645323	SK-N-SH	brain:	n/a	n/a
16	REST	chr1:47644744-47645167	A549	lung:	n/a	n/a
17	ATF3	chr1:47644780-47645219	A549	lung:	n/a	n/a
18	POLR2A	chr1:47644646-47645432	Hela-S3	cervix:	n/a	n/a
19	PAX5	chr1:47644805-47645195	GM12878	blood:	n/a	n/a
20	SRF	chr1:47644638-47645201	MCF-7	breast:	n/a	n/a
21	YY1	chr1:47644681-47645244	H1-hESC	embryonic stem cell:	n/a	n/a
22	EP300	chr1:47644763-47645097	HepG2	liver:	n/a	n/a
23	SRF	chr1:47644746-47645149	K562	blood:	n/a	n/a
24	CTCF	chr1:47644900-47645050	GM12867	blood:	n/a	n/a
25	POLR2A	chr1:47644713-47645173	GM12878	blood:	n/a	n/a
26	CTCF	chr1:47644900-47645050	GM12864	blood:	n/a	n/a
27	POLR2A	chr1:47644767-47645125	GM12878	blood:	n/a	n/a
28	MXI1	chr1:47644730-47645151	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZNF143	chr1:47644555-47645143	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr1:47644880-47645030	GM12869	blood:	n/a	n/a
31	MAZ	chr1:47644837-47645219	HepG2	liver:	n/a	n/a
32	MTA3	chr1:47644505-47645353	GM12878	blood:	n/a	n/a
33	CTCF	chr1:47644839-47645128	Gliobla	brain:	n/a	n/a
34	POLR2A	chr1:47644730-47645157	HCT-116	colon:	n/a	n/a
35	POLR2A	chr1:47644399-47645466	GM12891	blood:	n/a	n/a
36	CTCF	chr1:47644821-47645148	GM12878	blood:	n/a	n/a
37	PML	chr1:47644720-47645222	K562	blood:	n/a	n/a
38	MAX	chr1:47644620-47645365	ECC-1	luminal epithelium:	n/a	n/a
39	BHLHE40	chr1:47644620-47645305	K562	blood:	n/a	n/a
40	CTCF	chr1:47644880-47645030	HMF	breast:	n/a	n/a
41	SRF	chr1:47644541-47645364	HCT-116	colon:	n/a	n/a
42	RAD21	chr1:47644814-47645241	K562	blood:	n/a	n/a
43	TBL1XR1	chr1:47644590-47645228	K562	blood:	n/a	n/a
44	CHD1	chr1:47644847-47645158	H1-hESC	embryonic stem cell:	n/a	n/a
45	ARID3A	chr1:47644782-47645244	HepG2	liver:	n/a	n/a
46	CTCF	chr1:47644880-47645030	GM12868	blood:	n/a	n/a
47	ELF1	chr1:47644611-47645272	SK-N-SH	brain:	n/a	n/a
48	CHD2	chr1:47644629-47645162	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr1:47644772-47645190	GM12892	blood:	n/a	n/a
50	GTF2F1	chr1:47644772-47645124	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:47644372..47645188-chr14:55518016..55518529,2	HCT-116	colon:
2	chr1:47644710..47646624-chr1:47650334..47651868,2	MCF-7	breast:
3	chr1:47644503..47645102-chr5:43120843..43121679,2	Hela-S3	cervix:
4	chr1:47643313..47646101-chr1:47777883..47779835,2	K562	blood:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP4A22-2	chr1:47644290-47645110	XLOC_000175
2	lnc-PDZK1IP1-2	chr1:47644862-47644943	XLOC_000820
3	lnc-PDZK1IP1-2	chr1:47644862-47644943	ENSG00000225506
4	lnc-PDZK1IP1-2	chr1:47644862-47646045	NONHSAT003055
5	lnc-CYP4A22-2	chr1:47644809-47645336	NONHSAT003058
6	lnc-CYP4A22-2	chr1:47644220-47645110	NONHSAT003056
7	lnc-CYP4A22-2	chr1:47644220-47645110	NONHSAT003057

No data

Variant related genes	Relation type
LINC00853	TF binding region
ENSG00000168175	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000123473	Chromatin interaction
ENSG00000162366	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10890446	0.81[TSI][hapmap]
rs11211439	0.83[TSI][hapmap]
rs12022635	0.81[TSI][hapmap]
rs12564635	0.83[TSI][hapmap]
rs1393667	0.81[TSI][hapmap]
rs2742079	0.92[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2798352	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs9793202	0.81[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47641600-47645000	Weak transcription	Fetal Lung	lung
2	chr1:47644200-47645000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:47644200-47645000	Active TSS	GM12878-XiMat	blood
4	chr1:47644200-47645400	Active TSS	Hela-S3	cervix
5	chr1:47644200-47646800	Flanking Active TSS	K562	blood
6	chr1:47644200-47647400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:47644400-47645000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:47644400-47645000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:47644400-47645000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:47644400-47645000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:47644400-47645000	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:47644400-47645000	Enhancers	Placenta	Placenta
13	chr1:47644400-47645200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:47644400-47645200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:47644400-47645200	Active TSS	HSMMtube	muscle
16	chr1:47644400-47645400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:47644400-47645400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:47644400-47645400	Active TSS	A549	lung
19	chr1:47644400-47645600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:47644400-47645600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:47644400-47645600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:47644400-47645800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:47644400-47645800	Flanking Active TSS	Osteobl	bone
24	chr1:47644400-47646000	Enhancers	Spleen	Spleen
25	chr1:47644400-47646400	Weak transcription	Gastric	stomach
26	chr1:47644600-47645000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:47644600-47645000	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:47644600-47645000	Active TSS	Primary hematopoietic stem cells	blood
29	chr1:47644600-47645000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:47644600-47645000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:47644600-47645000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:47644600-47645000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:47644600-47645000	Active TSS	Adipose Nuclei	Adipose
34	chr1:47644600-47645000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:47644600-47645000	Active TSS	Duodenum Mucosa	Duodenum
36	chr1:47644600-47645000	Active TSS	Fetal Kidney	kidney
37	chr1:47644600-47645000	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:47644600-47645200	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr1:47644600-47645200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:47644600-47645200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:47644600-47645200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:47644600-47645200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:47644600-47645200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:47644600-47645200	Active TSS	Brain Anterior Caudate	brain
45	chr1:47644600-47645200	Active TSS	Fetal Intestine Small	intestine
46	chr1:47644600-47645200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr1:47644600-47645400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr1:47644600-47645400	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr1:47644600-47645400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:47644600-47645400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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