Variant report

Variant	rs6425537
Chromosome Location	chr1:179334252-179334253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179333806-179335727	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:179333903-179335412	GM19193	blood:	n/a	n/a
3	POLR2A	chr1:179334213-179335399	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:179334140-179335437	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:179334040-179335557	GM12892	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:179334251-179334301	CMK	blood:	n/a
2	chr1:179334251-179334301	GM12878	blood:	n/a
3	chr1:179334251-179334301	GM06990	blood:	n/a
4	chr1:179334251-179334301	RPTEC	kidney:	n/a
5	chr1:179334251-179334301	HUVEC	blood vessel:	n/a
6	chr1:179334251-179334301	HIPEpiC	eye:	n/a
7	chr1:179334251-179334301	AoSMC	blood vessel:	n/a
8	chr1:179334251-179334301	HRPEpiC	eye:	n/a
9	chr1:179334251-179334301	GM12892	blood:	n/a
10	chr1:179334251-179334301	GM19239	blood:	n/a
11	chr1:179334251-179334301	IMR90	lung:	fetal
12	chr1:179334251-179334301	SK-N-SH	brain:	n/a
13	chr1:179334251-179334301	ovcar-3	ovarian:	n/a
14	chr1:179334251-179334301	NB4	blood:	n/a
15	chr1:179334251-179334301	Hela-S3	cervix:	n/a
16	chr1:179334251-179334301	BJ	skin:	n/a
17	chr1:179334251-179334301	U87	brain:	n/a
18	chr1:179334251-179334301	SK-N-SH_RA	brain:	n/a
19	chr1:179334251-179334301	Hepatocyte	liver:	n/a
20	chr1:179334251-179334301	PFSK-1	brain:	n/a
21	chr1:179334251-179334301	AG10803	skin:	n/a
22	chr1:179334251-179334301	LNCaP	prostate:	n/a
23	chr1:179334251-179334301	NH-A	brain:	n/a
24	chr1:179334251-179334301	HCPEpiC	choroid plexus:	n/a
25	chr1:179334251-179334301	SKMC	muscle:	n/a
26	chr1:179334251-179334301	AG04449	skin:	fetal
27	chr1:179334251-179334301	T-47D	breast:	n/a
28	chr1:179334251-179334301	HEEpiC	esophagus:	n/a
29	chr1:179334251-179334301	HNPCEpiC	eye:	n/a
30	chr1:179334251-179334301	HCF	heart:	n/a
31	chr1:179334251-179334301	H1-hESC	embryonic stem cell:	embryo
32	chr1:179334251-179334301	HRE	kidney:	n/a
33	chr1:179334251-179334301	NHDF-neo	bronchial:	n/a
34	chr1:179334251-179334301	HCT-116	colon:	n/a
35	chr1:179334251-179334301	SAEC	small airway:	n/a
36	chr1:179334251-179334301	MCF-7	breast:	n/a
37	chr1:179334251-179334301	AG04450	lung:	fetal
38	chr1:179334251-179334301	MCF10A-Er-Src	breast:	n/a
39	chr1:179334251-179334301	NHBE	bronchial:	n/a
40	chr1:179334251-179334301	SK-N-MC	brain:	n/a
41	chr1:179334251-179334301	ECC-1	luminal epithelium:	n/a
42	chr1:179334251-179334301	HCM	heart:	n/a
43	chr1:179334251-179334301	HepG2	liver:	n/a
44	chr1:179334251-179334301	K562	blood:	n/a
45	chr1:179334251-179334301	HRCEpiC	kidney:	n/a
46	chr1:179334251-179334301	PrEC	prostate:	n/a
47	chr1:179334251-179334301	ProgFib	skin:	n/a
48	chr1:179334251-179334301	A549	lung:	n/a
49	chr1:179334251-179334301	Caco-2	colon:	n/a
50	chr1:179334251-179334301	HEK293	kidney:	embryo

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179049160..179052033-chr1:179333339..179335895,3	K562	blood:
3	chr1:179334248..179334935-chr18:77439530..77440162,2	Hela-S3	cervix:
4	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
5	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
6	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:
7	chr1:179048972..179052099-chr1:179331450..179336701,5	MCF-7	breast:
8	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

No data

Variant related genes	Relation type
AXDND1	TF binding region
AXDND1	CpG island
ENSG00000162779	Chromatin interaction
ENSG00000060069	Chromatin interaction
ENSG00000057252	Chromatin interaction
ENSG00000143322	Chromatin interaction
ENSG00000186283	Chromatin interaction
ENSG00000178412	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10753192	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798662	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798665	0.98[EUR][1000 genomes]
rs10798670	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913731	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913732	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913733	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913742	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913758	0.81[ASN][1000 genomes]
rs12047160	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12073906	0.81[ASN][1000 genomes]
rs12073970	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12117333	0.98[EUR][1000 genomes]
rs12118625	0.81[ASN][1000 genomes]
rs12138619	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12144580	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13306728	0.98[EUR][1000 genomes]
rs13306731	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13374852	0.90[ASN][1000 genomes]
rs16854009	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753526	0.98[EUR][1000 genomes]
rs4077551	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4077552	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41308413	0.98[EUR][1000 genomes]
rs41310929	0.98[EUR][1000 genomes]
rs41315575	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4394601	0.82[ASN][1000 genomes]
rs59334094	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61824395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7523799	0.98[EUR][1000 genomes]
rs9660720	0.81[ASN][1000 genomes]
rs975025	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3523650	chr1:179328529-179335027	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	esv3523651	chr1:179328979-179334877	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv3523653	chr1:179328979-179334877	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv20900	chr1:179329828-179335094	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv548284	chr1:179329899-179334801	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv548285	chr1:179329899-179334934	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv3371887	chr1:179330029-179334927	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv548289	chr1:179330173-179334801	Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
14	nsv548292	chr1:179330576-179334801	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
15	nsv548294	chr1:179330932-179334801	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
16	nsv548296	chr1:179330984-179334801	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:179312600-179334400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:179314800-179334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:179315000-179334400	Weak transcription	Brain Substantia Nigra	brain
5	chr1:179315000-179334400	Weak transcription	Left Ventricle	heart
6	chr1:179315400-179334400	Weak transcription	Fetal Kidney	kidney
7	chr1:179315600-179334400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:179316000-179334400	Weak transcription	Fetal Brain Female	brain
9	chr1:179316000-179334400	Weak transcription	Ovary	ovary
10	chr1:179317600-179334400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:179319200-179334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:179320000-179334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:179320800-179334400	Weak transcription	Fetal Lung	lung
14	chr1:179321200-179334400	Weak transcription	Fetal Stomach	stomach
15	chr1:179321200-179334400	Weak transcription	Lung	lung
16	chr1:179323000-179334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:179323000-179334400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:179323000-179334400	Weak transcription	NH-A	brain
19	chr1:179323000-179334400	Weak transcription	Osteobl	bone
20	chr1:179323200-179334400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:179323200-179334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:179323200-179334400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:179323200-179334400	Weak transcription	Fetal Heart	heart
24	chr1:179323200-179334400	Weak transcription	Fetal Intestine Large	intestine
25	chr1:179323600-179334400	Weak transcription	NHLF	lung
26	chr1:179324200-179334400	Weak transcription	Hela-S3	cervix
27	chr1:179324200-179334400	Weak transcription	HUVEC	blood vessel
28	chr1:179324200-179334400	Weak transcription	NHDF-Ad	bronchial
29	chr1:179324400-179334400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:179324400-179334400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:179324400-179334400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:179324400-179334400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:179324400-179334600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:179324800-179334400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:179324800-179334400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:179325200-179334400	Weak transcription	Primary T cells from cord blood	blood
37	chr1:179325200-179334400	Weak transcription	Liver	Liver
38	chr1:179331400-179334400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:179332800-179334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:179333200-179334400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:179334000-179334400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:179334000-179334400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr1:179334000-179334400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:179334000-179334400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr1:179334000-179334400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:179334000-179334400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr1:179334000-179334600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:179334000-179334600	Enhancers	Spleen	Spleen
49	chr1:179334000-179334600	Enhancers	HepG2	liver
50	chr1:179334000-179334800	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links