Variant report

Variant	rs13200047
Chromosome Location	chr6:109633244-109633245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109631513..109637347-chr6:109638223..109642715,6	K562	blood:
2	chr6:109629394..109632437-chr6:109632467..109635413,3	K562	blood:

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1008084	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11153165	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153166	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153167	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751953	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757567	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11961369	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11966072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1260595	0.83[CEU][hapmap]
rs12664455	0.95[ASN][1000 genomes]
rs13191948	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13195500	0.87[EUR][1000 genomes]
rs13196219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196590	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs13202939	0.88[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs13203155	0.88[ASN][1000 genomes]
rs13219432	0.94[ASN][1000 genomes]
rs13219561	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1341271	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1546723	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1741930	0.80[CEU][hapmap]
rs2884036	0.88[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs351719	0.85[TSI][hapmap]
rs351724	0.88[CEU][hapmap]
rs351725	0.88[CEU][hapmap]
rs351728	0.88[CEU][hapmap]
rs351736	0.84[CEU][hapmap]
rs351737	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs35757653	0.88[EUR][1000 genomes]
rs35849756	0.88[EUR][1000 genomes]
rs368467	0.80[CEU][hapmap]
rs377436	0.85[TSI][hapmap]
rs396000	0.80[CEU][hapmap]
rs419106	0.80[CEU][hapmap]
rs422113	0.85[TSI][hapmap]
rs4301336	0.88[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs446974	0.85[TSI][hapmap]
rs449736	0.85[TSI][hapmap]
rs4548045	0.91[ASN][1000 genomes]
rs5005289	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs55677234	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566164	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs59272337	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59502176	0.88[EUR][1000 genomes]
rs59673	0.85[TSI][hapmap]
rs6568569	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6568570	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6568571	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6919423	0.88[CEU][hapmap]
rs6925339	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs7748918	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7773490	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830554	0.85[TSI][hapmap]
rs9374076	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374080	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9374081	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386779	0.91[ASN][1000 genomes]
rs9386795	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9386796	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9400265	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9400272	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9400273	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9400276	0.88[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs9480924	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9487023	0.86[ASN][1000 genomes]
rs9487048	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9487049	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487051	0.94[ASN][1000 genomes]
rs9487052	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13200047	KIAA1919	cis	cerebellum	SCAN
rs13200047	ATG5	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109619400-109638000	Weak transcription	HepG2	liver
2	chr6:109621600-109634000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:109625800-109634200	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:109626200-109634200	Weak transcription	Psoas Muscle	Psoas
5	chr6:109626200-109638800	Weak transcription	Thymus	Thymus
6	chr6:109627600-109639000	Weak transcription	Left Ventricle	heart
7	chr6:109629600-109634000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:109629600-109639800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109629600-109654000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:109630200-109634400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:109630800-109636200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:109630800-109636200	Weak transcription	Fetal Intestine Large	intestine
13	chr6:109631000-109636200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:109631200-109633600	Weak transcription	Stomach Mucosa	stomach
15	chr6:109631600-109634200	Weak transcription	K562	blood
16	chr6:109631600-109636200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:109632000-109633800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:109632400-109633400	Enhancers	NHDF-Ad	bronchial

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