Variant report

Variant	rs59849608
Chromosome Location	chr1:169456717-169456718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:169453845-169456810	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:169452374-169456758	MCF10A-Er-Src	breast:	n/a	n/a
3	ATF3	chr1:169456443-169456736	K562	blood:	n/a	n/a
4	KAP1	chr1:169455068-169457749	HEK293	kidney:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
5	RFX5	chr1:169454125-169456976	SK-N-SH	brain:	n/a	chr1:169455259-169455268
6	CUX1	chr1:169456433-169456914	K562	blood:	n/a	n/a
7	KAP1	chr1:169455192-169456918	U2OS	brain:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
8	POLR2A	chr1:169451926-169456727	IMR90	lung:	n/a	n/a
9	CHD1	chr1:169452645-169456936	IMR90	lung:	n/a	chr1:169453020-169453027 chr1:169455009-169455019 chr1:169454476-169454486
10	JUND	chr1:169456367-169456751	HepG2	liver:	n/a	n/a
11	JUND	chr1:169454438-169456748	K562	blood:	n/a	chr1:169455928-169455939
12	JUN	chr1:169456373-169456728	HepG2	liver:	n/a	chr1:169456556-169456569

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	chr1:169456428..169460568-chr1:169464667..169468195,6	K562	blood:
4	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

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

Variant related genes	Relation type
SLC19A2	TF binding region
ENSG00000000460	Chromatin interaction
ENSG00000198734	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11589952	1.00[ASN][1000 genomes]
rs12029101	0.88[AMR][1000 genomes]
rs17518769	1.00[ASN][1000 genomes]
rs17577986	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169448000-169457000	Active TSS	Right Ventricle	heart
2	chr1:169451600-169457000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:169452600-169457000	Active TSS	Left Ventricle	heart
4	chr1:169453600-169457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:169454400-169458400	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:169455600-169457000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:169455600-169457400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:169455800-169456800	Flanking Active TSS	Fetal Heart	heart
10	chr1:169455800-169456800	Flanking Active TSS	Fetal Stomach	stomach
11	chr1:169455800-169456800	Flanking Active TSS	Hela-S3	cervix
12	chr1:169455800-169456800	Flanking Active TSS	HSMM	muscle
13	chr1:169455800-169457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:169455800-169457200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:169455800-169457200	Flanking Active TSS	HSMMtube	muscle
16	chr1:169455800-169457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:169455800-169457800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:169455800-169461400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:169456000-169456800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:169456000-169456800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:169456000-169456800	Flanking Active TSS	K562	blood
22	chr1:169456000-169457000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:169456000-169457000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:169456000-169457600	Flanking Active TSS	Liver	Liver
25	chr1:169456000-169460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:169456200-169456800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:169456200-169456800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:169456200-169456800	Enhancers	Stomach Mucosa	stomach
29	chr1:169456200-169457000	Weak transcription	Pancreas	Pancrea
30	chr1:169456200-169457000	Flanking Active TSS	HepG2	liver
31	chr1:169456200-169457200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:169456200-169457200	Enhancers	Fetal Brain Male	brain
33	chr1:169456200-169457800	Enhancers	Fetal Muscle Leg	muscle
34	chr1:169456200-169457800	Enhancers	Small Intestine	intestine
35	chr1:169456200-169464000	Weak transcription	Esophagus	oesophagus
36	chr1:169456400-169456800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:169456400-169456800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:169456400-169456800	Enhancers	Colon Smooth Muscle	Colon
39	chr1:169456400-169456800	Enhancers	Fetal Brain Female	brain
40	chr1:169456400-169456800	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:169456400-169456800	Enhancers	HUVEC	blood vessel
42	chr1:169456400-169457000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:169456400-169457000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:169456400-169457000	Enhancers	Fetal Intestine Small	intestine
45	chr1:169456400-169457000	Weak transcription	Right Atrium	heart
46	chr1:169456400-169457000	Enhancers	GM12878-XiMat	blood
47	chr1:169456400-169457200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:169456400-169457200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:169456400-169457200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:169456400-169457200	Enhancers	Brain Anterior Caudate	brain

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