Variant report

Variant	rs2986090
Chromosome Location	chr13:111309617-111309618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111308870..111310970-chr13:111364817..111367512,2	MCF-7	breast:
2	chr13:111302128..111303846-chr13:111308672..111310987,2	K562	blood:
3	chr13:111304729..111307376-chr13:111307813..111310341,2	K562	blood:

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2251314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2478465	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2478466	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2986085	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986086	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986325	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2986326	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366571	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369466	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs379114	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs384385	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388532	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389189	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs396523	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411771	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418321	0.88[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs422087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs424376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs424725	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs433080	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436283	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs451575	0.92[YRI][hapmap]
rs9588224	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
2	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
10	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
11	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
12	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
13	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv901013	chr13:111291192-111340342	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
15	nsv901014	chr13:111302922-111380684	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	197 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2986090	CARS2	cis	lymphoblastoid	seeQTL
rs2986090	TUBGCP3	cis	parietal	SCAN
rs2986090	PCID2	cis	cerebellum	SCAN
rs2986090	ARHGEF7	cis	cerebellum	SCAN
rs2986090	AL139385.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
2	chr13:111282800-111310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:111287400-111310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:111287800-111309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:111289400-111312000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr13:111289600-111310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:111293400-111314800	Weak transcription	HUVEC	blood vessel
8	chr13:111294000-111311800	Weak transcription	Fetal Kidney	kidney
9	chr13:111296000-111311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:111296600-111311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:111296800-111310000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:111296800-111310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr13:111297200-111310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:111297200-111313800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr13:111297600-111310000	Strong transcription	Fetal Intestine Small	intestine
16	chr13:111297600-111314400	Strong transcription	Fetal Intestine Large	intestine
17	chr13:111297800-111310600	Strong transcription	Fetal Stomach	stomach
18	chr13:111297800-111311400	Strong transcription	Fetal Muscle Leg	muscle
19	chr13:111297800-111317200	Weak transcription	Colon Smooth Muscle	Colon
20	chr13:111297800-111336400	Weak transcription	Small Intestine	intestine
21	chr13:111298000-111310200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:111298000-111320400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:111298200-111309800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:111298400-111310000	Weak transcription	A549	lung
25	chr13:111301200-111315600	Weak transcription	K562	blood
26	chr13:111301200-111322800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:111301600-111311400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:111301600-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr13:111301600-111324400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr13:111301800-111313600	Weak transcription	Fetal Brain Male	brain
31	chr13:111302000-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:111302200-111351400	Weak transcription	Stomach Mucosa	stomach
33	chr13:111303200-111314000	Weak transcription	Right Ventricle	heart
34	chr13:111303200-111314400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr13:111303400-111310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr13:111303400-111310200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr13:111303400-111314000	Weak transcription	Left Ventricle	heart
38	chr13:111303400-111314200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr13:111303400-111315600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr13:111303400-111327800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:111303600-111310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:111303600-111312400	Weak transcription	Brain Angular Gyrus	brain
43	chr13:111303800-111310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr13:111303800-111310000	Weak transcription	Fetal Lung	lung
45	chr13:111303800-111310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:111303800-111313800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr13:111304000-111311400	Weak transcription	NHDF-Ad	bronchial
48	chr13:111304000-111313400	Weak transcription	Brain Substantia Nigra	brain
49	chr13:111304400-111310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:111304800-111310200	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links