Variant report

Variant	rs10898414
Chromosome Location	chr11:85521117-85521118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85393932..85396795-chr11:85520364..85521949,2	MCF-7	breast:
2	chr11:85374332..85377604-chr11:85518032..85524824,7	MCF-7	breast:
3	chr11:85520346..85521861-chr11:85552981..85555359,2	MCF-7	breast:
4	chr11:85428619..85430275-chr11:85519411..85522192,2	MCF-7	breast:
5	chr11:85520588..85523121-chr11:85904931..85907542,2	MCF-7	breast:
6	chr11:85519803..85521941-chr11:85564201..85565920,2	MCF-7	breast:
7	chr11:85397382..85399853-chr11:85520148..85522002,2	MCF-7	breast:
8	chr11:85411666..85413624-chr11:85519059..85521959,2	MCF-7	breast:
9	chr11:85467606..85469318-chr11:85519137..85521764,2	MCF-7	breast:
10	chr11:85520681..85523600-chr11:85778386..85780657,2	MCF-7	breast:
11	chr11:85371938..85377336-chr11:85519037..85522510,5	MCF-7	breast:
12	chr11:85520966..85522059-chr11:85536950..85537673,3	MCF-7	breast:
13	chr11:85520161..85523649-chr11:85564385..85567428,4	MCF-7	breast:
14	chr11:85520628..85521546-chr11:85565642..85566152,2	MCF-7	breast:
15	chr11:85434348..85438681-chr11:85520824..85523815,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215504	Chromatin interaction
ENSG00000254502	Chromatin interaction
ENSG00000137501	Chromatin interaction
ENSG00000137504	Chromatin interaction
ENSG00000150676	Chromatin interaction
ENSG00000073921	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10898406	0.87[ASN][1000 genomes]
rs10898410	0.84[ASN][1000 genomes]
rs10898413	0.84[ASN][1000 genomes]
rs10898415	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11606656	0.84[ASN][1000 genomes]
rs12362853	0.87[ASN][1000 genomes]
rs1445497	0.88[ASN][1000 genomes]
rs1481700	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1893163	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2008890	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2044391	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2374683	0.84[ASN][1000 genomes]
rs485485	0.83[ASN][1000 genomes]
rs493078	0.82[ASN][1000 genomes]
rs4944538	0.84[ASN][1000 genomes]
rs556918	0.87[ASN][1000 genomes]
rs570394	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs575013	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs623120	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs630613	0.81[ASN][1000 genomes]
rs644972	0.81[ASN][1000 genomes]
rs652615	0.82[ASN][1000 genomes]
rs667275	0.82[ASN][1000 genomes]
rs683105	0.82[ASN][1000 genomes]
rs7103790	0.82[ASN][1000 genomes]
rs7123846	0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10898414	SYTL2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85518200-85521200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:85518600-85521200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:85518800-85521200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:85519000-85521200	Weak transcription	NHEK	skin
5	chr11:85520000-85521200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr11:85520000-85521400	Active TSS	Colonic Mucosa	Colon
7	chr11:85520000-85521600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:85520000-85521800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr11:85520000-85522400	Active TSS	Stomach Mucosa	stomach
10	chr11:85520200-85521200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr11:85520200-85521400	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:85520200-85521400	Active TSS	Rectal Smooth Muscle	rectum
13	chr11:85520200-85521400	Enhancers	HMEC	breast
14	chr11:85520200-85521400	Enhancers	HSMMtube	muscle
15	chr11:85520200-85522000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:85520200-85522000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:85520200-85522000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr11:85520200-85522200	Active TSS	Gastric	stomach
19	chr11:85520400-85521200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:85520400-85521400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:85520400-85521600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:85520400-85521600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:85520400-85521600	Weak transcription	Aorta	Aorta
24	chr11:85520400-85521600	Active TSS	Stomach Smooth Muscle	stomach
25	chr11:85520400-85521600	Enhancers	Spleen	Spleen
26	chr11:85520400-85522000	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr11:85520400-85522600	Enhancers	Fetal Brain Male	brain
28	chr11:85520400-85522800	Bivalent/Poised TSS	Thymus	Thymus
29	chr11:85520600-85521200	Enhancers	Fetal Lung	lung
30	chr11:85520600-85521400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr11:85520600-85521400	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:85520600-85521400	Enhancers	Fetal Heart	heart
33	chr11:85520600-85521600	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr11:85520600-85522000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:85520600-85522000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr11:85520600-85522000	Flanking Active TSS	HSMM	muscle
37	chr11:85520600-85522600	Active TSS	NHDF-Ad	bronchial
38	chr11:85520600-85523600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr11:85520800-85521200	Enhancers	Primary hematopoietic stem cells	blood
40	chr11:85520800-85521200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr11:85520800-85521200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr11:85520800-85521200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr11:85520800-85521200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:85520800-85521200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:85520800-85521200	Active TSS	Adipose Nuclei	Adipose
46	chr11:85520800-85521200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr11:85520800-85521200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr11:85520800-85521200	Flanking Active TSS	NHLF	lung
49	chr11:85520800-85521400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:85520800-85521400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links