Variant report

Variant	rs4699192
Chromosome Location	chr4:106578151-106578152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106577459..106579904-chr4:106585489..106587073,2	K562	blood:
2	chr4:106575884..106578355-chr4:106580539..106582862,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10019217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030620	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10049527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10516522	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1157775	0.85[ASN][1000 genomes]
rs11930244	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11930965	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11942577	0.86[CHB][hapmap]
rs12504088	0.80[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12511885	0.80[CEU][hapmap];0.81[ASN][1000 genomes]
rs12512339	0.95[ASN][1000 genomes]
rs13110070	1.00[ASN][1000 genomes]
rs13145251	0.97[ASN][1000 genomes]
rs17035917	0.86[CEU][hapmap]
rs17036093	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17036097	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17036102	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17036254	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2193852	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2193854	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs28370551	0.85[ASN][1000 genomes]
rs28391170	0.85[ASN][1000 genomes]
rs28450989	0.85[ASN][1000 genomes]
rs28559909	0.88[ASN][1000 genomes]
rs28698939	1.00[ASN][1000 genomes]
rs3796926	0.85[ASN][1000 genomes]
rs4235415	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4490460	0.85[ASN][1000 genomes]
rs4698950	0.93[ASN][1000 genomes]
rs4698951	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4699193	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4699194	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4699195	0.85[ASN][1000 genomes]
rs4699197	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4699198	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4699199	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs56849622	0.80[ASN][1000 genomes]
rs58388061	0.81[ASN][1000 genomes]
rs58914657	0.97[ASN][1000 genomes]
rs60774107	0.83[ASN][1000 genomes]
rs6817029	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6820671	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6825379	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7658055	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7659526	0.80[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7696836	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697619	0.81[ASN][1000 genomes]
rs989775	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3467298	chr4:106577722-106583287	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3467299	chr4:106577722-106583287	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv14749	chr4:106577867-106583120	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4699192	SPTLC2	trans	parietal	SCAN
rs4699192	INTS12	cis	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106559400-106580000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:106559400-106580200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:106559400-106602800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:106569800-106600400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:106574400-106585400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:106576600-106581400	Strong transcription	Fetal Intestine Large	intestine
7	chr4:106577800-106578200	Strong transcription	Pancreas	Pancrea
8	chr4:106577800-106578600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr4:106577800-106579200	Enhancers	NHEK	skin
10	chr4:106578000-106578600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:106578000-106579000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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