Variant report

Variant	rs11896520
Chromosome Location	chr2:99995517-99995518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10496336	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11885942	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11887935	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11893359	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12466114	0.81[AMR][1000 genomes]
rs12474305	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12479064	0.87[MEX][hapmap]
rs1823569	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs1922624	0.84[GIH][hapmap]
rs2141907	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305352	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2309618	1.00[CEU][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28369945	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28382977	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3087403	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3792143	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3792150	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4341989	0.95[CEU][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4851203	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4851207	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4851210	0.81[AMR][1000 genomes]
rs4851212	0.88[GIH][hapmap]
rs61436115	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62153852	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62155769	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62155807	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6714650	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6748200	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs737094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995617	0.87[ASW][hapmap];1.00[CHD][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking 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	28 gene(s)	inside rSNPs	diseases
4	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers 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	5 gene(s)	inside rSNPs	diseases
5	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11896520	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs11896520	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11896520	FAHD2B	cis	parietal	SCAN
rs11896520	LIPT1	cis	cerebellum	SCAN
rs11896520	LIPT1	cis	parietal	SCAN
rs11896520	ANKRD39	cis	cerebellum	SCAN
rs11896520	TSGA10	cis	parietal	SCAN
rs11896520	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
2	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
3	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:99976400-100003200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:99976600-100002400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:99977000-99996800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:99977000-100001000	Strong transcription	Primary B cells from cord blood	blood
10	chr2:99977000-100001400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:99977000-100003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:99977000-100003200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:99977000-100003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:99977000-100003800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:99977000-100003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:99977200-99996200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:99977600-99997000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:99977600-100002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:99977600-100003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:99977800-99996800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:99978200-99997200	Strong transcription	Placenta	Placenta
22	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
23	chr2:99978600-99995600	Weak transcription	Small Intestine	intestine
24	chr2:99979400-99999800	Strong transcription	Osteobl	bone
25	chr2:99979400-100001600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:99979400-100003600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:99979400-100004200	Strong transcription	Fetal Thymus	thymus
28	chr2:99979600-99997200	Strong transcription	Adipose Nuclei	Adipose
29	chr2:99979600-100002800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:99979600-100003200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:99979600-100009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:99979800-99996400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:99979800-100002200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:99979800-100002800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:99982800-100000400	Strong transcription	HSMM	muscle
36	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:99984600-99997200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:99985400-99996800	Strong transcription	Liver	Liver
39	chr2:99985600-100006800	Weak transcription	Colonic Mucosa	Colon
40	chr2:99985800-99998800	Weak transcription	Psoas Muscle	Psoas
41	chr2:99986000-99996800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:99986600-99997800	Strong transcription	HepG2	liver
43	chr2:99987400-99995800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:99987400-99999400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:99988000-99996600	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr2:99988000-100003200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:99988200-100001400	Strong transcription	K562	blood
48	chr2:99988400-100001400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr2:99988400-100001400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:99988600-99997200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links