Variant report

Variant	rs4309017
Chromosome Location	chr1:153828134-153828135
allele	A/G
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	RPC155	chr1:153828098-153828525	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153825891..153828741-chr1:153837301..153840342,3	K562	blood:

Variant related genes	Relation type
ENSG00000223599	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11264522	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264824	0.84[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1127092	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12023578	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12032520	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033532	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12039936	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12043354	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12044455	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12045838	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12726350	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072704	1.00[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297895	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33998934	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34579266	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34665499	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34752019	0.84[MEX][hapmap]
rs35036680	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35170146	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4323749	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61804837	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804838	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804839	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61805526	0.83[EUR][1000 genomes]
rs6427298	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427334	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671009	0.84[MEX][hapmap]
rs67579382	0.93[ASN][1000 genomes]
rs7527406	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9427246	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	233 gene(s)	inside rSNPs	diseases
7	esv1825076	chr1:153779296-153843413	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4309017	HAX1	cis	cerebellum	SCAN
rs4309017	HAX1	cis	lymphoblastoid	seeQTL
rs4309017	HAX1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153791800-153845600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:153800800-153830800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:153800800-153832600	Weak transcription	Aorta	Aorta
4	chr1:153800800-153832800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:153800800-153835600	Weak transcription	Ovary	ovary
6	chr1:153800800-153850800	Weak transcription	A549	lung
7	chr1:153800800-153852800	Weak transcription	Fetal Brain Female	brain
8	chr1:153800800-153852800	Weak transcription	Placenta	Placenta
9	chr1:153800800-153852800	Weak transcription	Left Ventricle	heart
10	chr1:153800800-153853000	Weak transcription	Fetal Kidney	kidney
11	chr1:153801200-153829800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:153801200-153829800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:153801600-153845800	Weak transcription	Lung	lung
14	chr1:153801800-153836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:153806200-153845400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:153814800-153828400	Weak transcription	NHDF-Ad	bronchial
17	chr1:153814800-153835200	Weak transcription	Osteobl	bone
18	chr1:153814800-153839000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:153814800-153848000	Weak transcription	Fetal Heart	heart
20	chr1:153814800-153853400	Weak transcription	HSMMtube	muscle
21	chr1:153816000-153844000	Weak transcription	Right Ventricle	heart
22	chr1:153816600-153836200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:153816800-153834600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:153821400-153832800	Weak transcription	Gastric	stomach
25	chr1:153821600-153839800	Weak transcription	Small Intestine	intestine
26	chr1:153822000-153836000	Weak transcription	Liver	Liver
27	chr1:153822000-153838600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:153822600-153839000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:153822600-153839400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:153822800-153853400	Weak transcription	HMEC	breast
31	chr1:153822800-153854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:153823200-153833600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:153823600-153845400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr1:153823800-153833600	Strong transcription	Dnd41	blood
35	chr1:153824000-153843600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:153825000-153840200	Weak transcription	NHEK	skin
37	chr1:153825200-153836600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:153825200-153838800	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:153825400-153836600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:153825600-153828400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:153825600-153830000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:153825600-153830000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:153825600-153833200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:153825600-153833200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:153825600-153838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:153825800-153828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:153825800-153828400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:153825800-153829200	Weak transcription	HSMM	muscle
49	chr1:153825800-153829600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:153825800-153836200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links