Variant report

Variant	rs2304343
Chromosome Location	chr11:85456849-85456850
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85452340..85455544-chr11:85456750..85459606,3	K562	blood:
2	chr11:85374586..85376226-chr11:85456033..85458381,2	K562	blood:
3	chr11:85456354..85459698-chr11:85460209..85463531,4	MCF-7	breast:
4	chr11:85456348..85458453-chr11:85459854..85462602,2	K562	blood:
5	chr11:85449141..85453316-chr11:85456820..85460896,4	MCF-7	breast:
6	chr11:85434029..85438059-chr11:85455702..85460015,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10501597	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898409	0.93[ASN][1000 genomes]
rs10898422	0.88[GIH][hapmap]
rs11234386	1.00[EUR][1000 genomes]
rs11234387	1.00[EUR][1000 genomes]
rs11234388	0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11234389	0.92[JPT][hapmap]
rs11234390	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11234391	0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11234392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234393	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234397	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234404	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11234408	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11234409	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11234413	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11234415	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11234416	1.00[EUR][1000 genomes]
rs11234418	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11234427	0.94[GIH][hapmap]
rs11234450	0.94[GIH][hapmap]
rs11234460	0.94[GIH][hapmap]
rs11234461	0.94[GIH][hapmap]
rs12286030	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12286206	1.00[EUR][1000 genomes]
rs12360932	0.94[GIH][hapmap]
rs12362209	0.94[GIH][hapmap]
rs12363624	0.94[GIH][hapmap]
rs12365370	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17148355	0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17208525	0.86[JPT][hapmap]
rs17208602	0.86[JPT][hapmap];1.00[MEX][hapmap]
rs17208616	0.92[JPT][hapmap]
rs17209127	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs17810701	0.86[JPT][hapmap]
rs17810766	0.86[JPT][hapmap];1.00[MEX][hapmap]
rs17810802	0.86[JPT][hapmap];1.00[MEX][hapmap]
rs17810855	1.00[JPT][hapmap]
rs17811120	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2044393	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2276018	0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2304342	0.86[JPT][hapmap]
rs36035618	1.00[AFR][1000 genomes]
rs3891432	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494119	0.86[JPT][hapmap]
rs616309	0.92[JPT][hapmap]
rs645798	0.92[JPT][hapmap]
rs678376	0.86[JPT][hapmap]
rs73518846	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv3471508	chr11:85429687-85472395	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3471519	chr11:85429687-85472395	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv555634	chr11:85430397-85464922	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv555635	chr11:85430397-85470893	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv555636	chr11:85431886-85465179	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1042192	chr11:85433687-85464922	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1039118	chr11:85433687-85468605	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv1039830	chr11:85433687-85470589	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1047001	chr11:85433687-85470941	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv1042942	chr11:85433687-85471132	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1052732	chr11:85434057-85468605	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv1048844	chr11:85434057-85470941	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1051644	chr11:85434057-85471132	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv555637	chr11:85435730-85470893	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv555638	chr11:85436303-85458076	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv555639	chr11:85436352-85495269	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1048750	chr11:85436840-85471132	Enhancers Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	esv2754674	chr11:85436852-85470852	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	esv2757459	chr11:85436868-85473347	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv541112	chr11:85436956-85468985	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	nsv541113	chr11:85437155-85468845	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	nsv555640	chr11:85456703-85464922	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2304343	SYTL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85430400-85459000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:85430400-85480400	Weak transcription	Aorta	Aorta
3	chr11:85430800-85459000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:85431800-85466600	Weak transcription	Brain Substantia Nigra	brain
5	chr11:85432000-85460800	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:85437600-85459800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:85437800-85458000	Weak transcription	HSMM	muscle
8	chr11:85441600-85460200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:85442200-85461000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:85444400-85461600	Weak transcription	Lung	lung
11	chr11:85445600-85459800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:85445600-85460200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:85447400-85459200	Weak transcription	NH-A	brain
14	chr11:85447400-85459400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:85447600-85459400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:85448000-85463600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:85448000-85480600	Weak transcription	Fetal Stomach	stomach
18	chr11:85448200-85460400	Weak transcription	NHLF	lung
19	chr11:85449200-85459800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:85449200-85478400	Weak transcription	Right Ventricle	heart
21	chr11:85451400-85457600	Enhancers	Fetal Intestine Small	intestine
22	chr11:85452000-85462600	Weak transcription	HSMMtube	muscle
23	chr11:85452400-85459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:85452400-85459400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:85452400-85461800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:85452800-85463000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:85453000-85460000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:85453000-85471000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:85454000-85458600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr11:85454200-85459000	Weak transcription	A549	lung
31	chr11:85454200-85461000	Weak transcription	Fetal Lung	lung
32	chr11:85454200-85462600	Weak transcription	Left Ventricle	heart
33	chr11:85454800-85457400	Enhancers	Colonic Mucosa	Colon
34	chr11:85455000-85470800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:85455600-85458800	Genic enhancers	Rectal Mucosa Donor 31	rectum
36	chr11:85455600-85459200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr11:85455800-85459000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:85455800-85461800	Enhancers	Stomach Mucosa	stomach
39	chr11:85456000-85458600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr11:85456200-85457600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr11:85456200-85458200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr11:85456200-85458600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:85456200-85458800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr11:85456200-85458800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr11:85456200-85460600	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr11:85456400-85457000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:85456400-85457000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:85456400-85457200	Bivalent Enhancer	Fetal Thymus	thymus
49	chr11:85456400-85457200	Enhancers	HUVEC	blood vessel
50	chr11:85456400-85457400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links