Variant report

Variant	rs10898410
Chromosome Location	chr11:85509806-85509807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85394543..85396055-chr11:85509684..85512654,2	MCF-7	breast:
2	chr11:85374466..85376383-chr11:85507229..85510885,4	MCF-7	breast:
3	chr11:85433629..85436258-chr11:85509690..85512364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10898406	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10898413	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10898414	0.84[ASN][1000 genomes]
rs10898415	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606656	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12362853	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1237203	0.83[MEX][hapmap]
rs1445497	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1481700	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17817179	0.88[CEU][hapmap]
rs1893163	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]
rs2008890	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044391	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2044392	0.87[ASN][1000 genomes]
rs2374683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs290173	0.80[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs290202	0.81[CEU][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs370385	0.81[JPT][hapmap]
rs485485	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491867	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs493078	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944538	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs496187	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs540063	0.81[CHB][hapmap]
rs550404	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs556669	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs556918	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580459	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs589327	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs592712	0.81[CEU][hapmap]
rs597480	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs630613	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs631410	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs641393	0.82[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap]
rs644972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs647912	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs652615	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs667275	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs679204	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes]
rs680498	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs683105	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7103790	0.83[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs7123846	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10898410	SYTL2	cis	multi-tissue	Pritchard
rs10898410	SYTL2	cis	Muscle Skeletal	GTEx
rs10898410	ME3	cis	cerebellum	SCAN
rs10898410	GRM5	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85491800-85517800	Weak transcription	NHLF	lung
2	chr11:85496400-85510600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr11:85499200-85510400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr11:85499200-85517200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr11:85499800-85517400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:85503200-85511800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:85503400-85510800	Weak transcription	Small Intestine	intestine
8	chr11:85503400-85513200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:85503400-85516400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr11:85506200-85514400	Weak transcription	Primary T cells from cord blood	blood
11	chr11:85507200-85510600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr11:85507200-85512600	Weak transcription	Fetal Kidney	kidney
13	chr11:85507400-85510000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:85509400-85510400	Enhancers	A549	lung
15	chr11:85509400-85512400	Enhancers	Stomach Mucosa	stomach
16	chr11:85509600-85510800	Enhancers	Fetal Muscle Leg	muscle
17	chr11:85509600-85512000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr11:85509600-85512200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:85509800-85510000	Enhancers	Primary T cells fromperipheralblood	blood
20	chr11:85509800-85510000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr11:85509800-85511400	Enhancers	Fetal Intestine Large	intestine
22	chr11:85509800-85511400	Enhancers	Fetal Intestine Small	intestine
23	chr11:85509800-85512000	Enhancers	Colonic Mucosa	Colon
24	chr11:85509800-85512800	Enhancers	Duodenum Mucosa	Duodenum
25	chr11:85509800-85520000	Weak transcription	HSMM	muscle

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