Variant report

Variant	rs13124696
Chromosome Location	chr4:57214366-57214367
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57210332..57213092-chr4:57213871..57215383,2	K562	blood:
2	chr4:57209917..57212599-chr4:57213686..57216147,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1042040	0.89[MEX][hapmap]
rs11728110	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11930159	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11943048	0.89[MEX][hapmap]
rs13102012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13102298	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13109030	0.85[CEU][hapmap]
rs13122196	0.85[CEU][hapmap]
rs13122832	0.85[CEU][hapmap]
rs13129188	0.85[CEU][hapmap]
rs13134963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13135046	0.88[ASN][1000 genomes]
rs13147132	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13148656	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs13150159	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13150967	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs17086759	0.82[JPT][hapmap]
rs17086773	0.82[JPT][hapmap]
rs2030364	0.83[EUR][1000 genomes]
rs2176785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733324	0.91[JPT][hapmap]
rs3733326	0.82[JPT][hapmap]
rs3796540	0.81[JPT][hapmap]
rs3796544	0.85[CEU][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap]
rs41498446	0.91[JPT][hapmap]
rs6554347	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554350	0.85[CEU][hapmap]
rs6554354	0.85[CEU][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap]
rs6811616	0.85[CEU][hapmap];0.89[MEX][hapmap]
rs6812222	0.85[CEU][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap]
rs6854758	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694439	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7695701	0.84[MEX][hapmap]
rs956275	0.94[MEX][hapmap]
rs9995463	0.84[CEU][hapmap]
rs9996468	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13124696	AASDH	cis	lymphoblastoid	seeQTL
rs13124696	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs13124696	AASDH	cis	Skin Sun Exposed Lower leg	GTEx
rs13124696	AASDH	cis	multi-tissue	Pritchard
rs13124696	AASDH	cis	parietal	SCAN
rs13124696	AASDH	cis	cerebellum	SCAN
rs13124696	AASDH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
2	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
4	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
5	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
6	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
7	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
8	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:57198800-57214400	Weak transcription	Gastric	stomach
10	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
12	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
13	chr4:57203200-57215000	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:57203200-57215600	Weak transcription	Pancreas	Pancrea
15	chr4:57203200-57235200	Weak transcription	Osteobl	bone
16	chr4:57203200-57251800	Weak transcription	A549	lung
17	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:57203600-57214400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:57204000-57216800	Weak transcription	Hela-S3	cervix
21	chr4:57204000-57252200	Weak transcription	NH-A	brain
22	chr4:57204200-57214400	Weak transcription	Primary B cells from cord blood	blood
23	chr4:57204200-57214400	Weak transcription	Fetal Thymus	thymus
24	chr4:57204200-57214400	Weak transcription	Dnd41	blood
25	chr4:57204200-57222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:57204200-57227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:57204200-57252200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:57204400-57214400	Weak transcription	Brain Angular Gyrus	brain
29	chr4:57204800-57214400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:57204800-57214400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:57204800-57214400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:57204800-57214400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:57204800-57214400	Weak transcription	Stomach Mucosa	stomach
34	chr4:57204800-57214800	Weak transcription	HSMM	muscle
35	chr4:57204800-57215200	Weak transcription	HSMMtube	muscle
36	chr4:57204800-57215400	Weak transcription	Psoas Muscle	Psoas
37	chr4:57204800-57223400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:57204800-57235400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr4:57204800-57251800	Weak transcription	Fetal Brain Male	brain
40	chr4:57205000-57214400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:57205000-57214400	Weak transcription	Fetal Intestine Large	intestine
42	chr4:57205000-57214400	Weak transcription	Fetal Lung	lung
43	chr4:57205000-57214400	Weak transcription	Ovary	ovary
44	chr4:57205000-57214600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:57205000-57214600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:57205000-57217200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr4:57205000-57223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:57205000-57228000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:57205200-57214400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:57205200-57214400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links