Variant report

Variant	rs2056926
Chromosome Location	chr1:169455435-169455436
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:506)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:506 , 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	USF1	chr1:169455083-169455501	A549	lung:	n/a	n/a
2	ETS1	chr1:169454689-169455506	K562	blood:	n/a	chr1:169455132-169455143
3	PML	chr1:169454817-169455676	MCF-7	breast:	n/a	n/a
4	TFAP2C	chr1:169454455-169455732	Hela-S3	cervix:	n/a	n/a
5	GTF2B	chr1:169454970-169455661	K562	blood:	n/a	n/a
6	USF1	chr1:169455105-169455454	A549	lung:	n/a	n/a
7	TBP	chr1:169454976-169455626	GM12878	blood:	n/a	n/a
8	CCNT2	chr1:169454604-169455681	K562	blood:	n/a	chr1:169455015-169455024
9	MXI1	chr1:169453845-169456810	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr1:169455300-169455450	AG09309	skin:	n/a	n/a
11	POLR2A	chr1:169454751-169455777	ProgFib	skin:	n/a	n/a
12	SP1	chr1:169454953-169455615	H1-hESC	embryonic stem cell:	n/a	chr1:169455014-169455026 chr1:169455015-169455024
13	GATA3	chr1:169454978-169455638	T-47D	breast:	n/a	n/a
14	SIN3AK20	chr1:169454997-169455555	HepG2	liver:	n/a	n/a
15	TAF1	chr1:169455055-169455605	PFSK-1	brain:	n/a	n/a
16	MYC	chr1:169454919-169455545	H1-hESC	embryonic stem cell:	n/a	n/a
17	FOXA1	chr1:169455009-169455679	HepG2	liver:	n/a	n/a
18	PBX3	chr1:169454978-169455661	A549	lung:	n/a	n/a
19	CTCF	chr1:169455006-169455637	IMR90	lung:	n/a	n/a
20	CHD1	chr1:169454918-169455619	GM12878	blood:	n/a	chr1:169455009-169455019
21	POLR2A	chr1:169454762-169455717	GM12878	blood:	n/a	n/a
22	TBL1XR1	chr1:169454706-169455491	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:169454742-169455787	SK-N-MC	brain:	n/a	n/a
24	CREB1	chr1:169455063-169455613	ECC-1	luminal epithelium:	n/a	n/a
25	NR3C1	chr1:169454716-169455742	A549	lung:	n/a	chr1:169455115-169455132
26	TAF1	chr1:169454739-169455717	Hela-S3	cervix:	n/a	n/a
27	USF1	chr1:169455058-169455564	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr1:169455092-169455541	K562	blood:	n/a	n/a
29	BRCA1	chr1:169454999-169456158	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr1:169454981-169455651	PFSK-1	brain:	n/a	n/a
31	USF2	chr1:169455082-169455585	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr1:169453879-169456142	Hela-S3	cervix:	n/a	n/a
33	TAF1	chr1:169454493-169455849	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr1:169454974-169455641	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr1:169455049-169455538	HepG2	liver:	n/a	n/a
36	MYC	chr1:169454014-169456207	MCF10A-Er-Src	breast:	n/a	n/a
37	BCLAF1	chr1:169455128-169455685	GM12878	blood:	n/a	n/a
38	SIX5	chr1:169455243-169456008	A549	lung:	n/a	n/a
39	POLR2A	chr1:169454469-169455761	MCF-7	breast:	n/a	n/a
40	IRF1	chr1:169455035-169455702	K562	blood:	n/a	n/a
41	POLR2A	chr1:169454437-169455995	K562	blood:	n/a	n/a
42	MAX	chr1:169455131-169455656	H1-hESC	embryonic stem cell:	n/a	n/a
43	NR3C1	chr1:169454767-169455828	A549	lung:	n/a	chr1:169455115-169455132
44	MAFK	chr1:169455301-169455608	HepG2	liver:	n/a	n/a
45	HEY1	chr1:169454401-169455707	K562	blood:	n/a	chr1:169454753-169454768 chr1:169454781-169454796 chr1:169454742-169454757
46	SP1	chr1:169454968-169455602	GM12878	blood:	n/a	chr1:169455014-169455026 chr1:169455015-169455024
47	E2F6	chr1:169454467-169455717	H1-hESC	embryonic stem cell:	n/a	chr1:169454770-169454782 chr1:169454768-169454783
48	POLR2A	chr1:169454976-169455613	HepG2	liver:	n/a	n/a
49	CREB1	chr1:169454989-169455609	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAF1	chr1:169454280-169455714	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:169455416-169455466	HPAEpiC	pulmonary alveolar:	n/a
2	chr1:169455409-169455459	K562	blood:	n/a
3	chr1:169455416-169455466	NHBE	bronchial:	n/a
4	chr1:169455409-169455459	GM06990	blood:	n/a
5	chr1:169455409-169455459	HCF	heart:	n/a
6	chr1:169455416-169455466	HCM	heart:	n/a
7	chr1:169455409-169455459	Caco-2	colon:	n/a
8	chr1:169455416-169455466	HUVEC	blood vessel:	n/a
9	chr1:169455416-169455466	HEK293	kidney:	embryo
10	chr1:169455416-169455466	SK-N-SH_RA	brain:	n/a
11	chr1:169455409-169455459	SK-N-SH_RA	brain:	n/a
12	chr1:169455409-169455459	NHDF-neo	bronchial:	n/a
13	chr1:169455409-169455459	BJ	skin:	n/a
14	chr1:169455409-169455459	AoSMC	blood vessel:	n/a
15	chr1:169455416-169455466	NB4	blood:	n/a
16	chr1:169455409-169455459	AG10803	skin:	n/a
17	chr1:169455409-169455459	NHBE	bronchial:	n/a
18	chr1:169455416-169455466	AG09319	gingival:	n/a
19	chr1:169455409-169455459	MCF-7	breast:	n/a
20	chr1:169455416-169455466	H1-hESC	embryonic stem cell:	embryo
21	chr1:169455416-169455466	NHDF-neo	bronchial:	n/a
22	chr1:169455416-169455466	PFSK-1	brain:	n/a
23	chr1:169455416-169455466	SAEC	small airway:	n/a
24	chr1:169455416-169455466	GM19239	blood:	n/a
25	chr1:169455409-169455459	HCM	heart:	n/a
26	chr1:169455416-169455466	AG04449	skin:	fetal
27	chr1:169455416-169455466	HRCEpiC	kidney:	n/a
28	chr1:169455409-169455459	AG04450	lung:	fetal
29	chr1:169455409-169455459	GM12892	blood:	n/a
30	chr1:169455416-169455466	SK-N-MC	brain:	n/a
31	chr1:169455416-169455466	HEEpiC	esophagus:	n/a
32	chr1:169455416-169455466	T-47D	breast:	n/a
33	chr1:169455416-169455466	HCPEpiC	choroid plexus:	n/a
34	chr1:169455409-169455459	HPAEpiC	pulmonary alveolar:	n/a
35	chr1:169455409-169455459	ovcar-3	ovarian:	n/a
36	chr1:169455409-169455459	BE2_C	brain:	n/a
37	chr1:169455416-169455466	NH-A	brain:	n/a
38	chr1:169455409-169455459	HepG2	liver:	n/a
39	chr1:169455416-169455466	A549	lung:	n/a
40	chr1:169455416-169455466	IMR90	lung:	fetal
41	chr1:169455409-169455459	HMEC	breast:	n/a
42	chr1:169455416-169455466	HMEC	breast:	n/a
43	chr1:169455416-169455466	HRPEpiC	eye:	n/a
44	chr1:169455409-169455459	HAEpiC	amniotic membrane:	n/a
45	chr1:169455409-169455459	RPTEC	kidney:	n/a
46	chr1:169455416-169455466	HCF	heart:	n/a
47	chr1:169455416-169455466	AG04450	lung:	fetal
48	chr1:169455416-169455466	HIPEpiC	eye:	n/a
49	chr1:169455409-169455459	SAEC	small airway:	n/a
50	chr1:169455409-169455459	HNPCEpiC	eye:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169455407..169455909-chr5:40625359..40625859,2	NB4	blood:
4	chr1:16840029..16840801-chr1:169454808..169455627,2	HCT-116	colon:
5	chr1:169454789..169455681-chr12:54385187..54385687,2	Hela-S3	cervix:
6	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BLZF1-2	chr1:169455353-169458414	NONHSAT007465
2	lnc-BLZF1-2	chr1:169455380-169456846	NONHSAT139913

No data

Variant related genes	Relation type
SLC19A2	TF binding region
SLC19A2	CpG island
ENSG00000000460	Chromatin interaction
ENSG00000207924	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10919175	0.84[JPT][hapmap]
rs12408451	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2157580	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2056926	NME7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
2	chr1:169450000-169456000	Active TSS	Psoas Muscle	Psoas
3	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:169452200-169456200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:169452600-169455600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
7	chr1:169452800-169455600	Active TSS	HepG2	liver
8	chr1:169452800-169456000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:169452800-169456000	Active TSS	Stomach Smooth Muscle	stomach
10	chr1:169452800-169456200	Active TSS	Ovary	ovary
11	chr1:169453200-169455800	Active TSS	Esophagus	oesophagus
12	chr1:169453200-169456000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:169453200-169456000	Active TSS	Placenta	Placenta
14	chr1:169453200-169456200	Active TSS	Pancreas	Pancrea
15	chr1:169453400-169455800	Active TSS	Fetal Stomach	stomach
16	chr1:169453400-169455800	Active TSS	Lung	lung
17	chr1:169453400-169456000	Active TSS	Colonic Mucosa	Colon
18	chr1:169453400-169456200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:169453400-169456600	Active TSS	Aorta	Aorta
20	chr1:169453600-169455800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:169453600-169456000	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:169453600-169456200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr1:169453800-169455600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:169453800-169455800	Active TSS	HSMM	muscle
27	chr1:169453800-169456000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:169453800-169456200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:169453800-169456400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr1:169453800-169456400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:169454000-169455600	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr1:169454000-169455800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:169454000-169456200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr1:169454000-169456200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:169454000-169456200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:169454200-169455600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr1:169454200-169455600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:169454200-169455600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr1:169454200-169455600	Active TSS	Gastric	stomach
40	chr1:169454200-169455600	Active TSS	Small Intestine	intestine
41	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:169454200-169455800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:169454200-169455800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:169454200-169455800	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:169454200-169455800	Active TSS	Brain Germinal Matrix	brain
46	chr1:169454200-169455800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:169454200-169455800	Active TSS	Hela-S3	cervix
48	chr1:169454200-169456000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:169454200-169456200	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:169454200-169456400	Active TSS	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links