Variant report

Variant	rs13008948
Chromosome Location	chr2:99921205-99921206
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99919697..99922118-chr2:99951528..99953553,2	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10779902	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123775	0.82[ASN][1000 genomes]
rs11123777	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123779	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674219	0.83[ASN][1000 genomes]
rs11676581	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11679115	0.83[ASN][1000 genomes]
rs11683651	0.83[ASN][1000 genomes]
rs11685870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11686535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687328	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11687870	0.84[ASN][1000 genomes]
rs11892472	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895206	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11897443	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11902994	0.83[ASN][1000 genomes]
rs12464535	0.83[ASN][1000 genomes]
rs12611687	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12615519	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12621141	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623540	0.83[ASN][1000 genomes]
rs13004376	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13007100	0.85[EUR][1000 genomes]
rs13009863	0.94[AMR][1000 genomes]
rs13009884	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13010416	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13011240	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13014360	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13016182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13017871	0.86[ASN][1000 genomes]
rs13018274	0.81[ASN][1000 genomes]
rs13019192	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13026997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028869	0.83[ASN][1000 genomes]
rs13033740	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376443	0.83[ASN][1000 genomes]
rs17022433	0.82[ASN][1000 genomes]
rs1807985	0.81[ASN][1000 genomes]
rs1825770	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1955393	0.82[ASN][1000 genomes]
rs2290256	0.80[ASN][1000 genomes]
rs3811555	0.86[ASN][1000 genomes]
rs4850899	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4850901	0.84[ASN][1000 genomes]
rs4850903	0.83[ASN][1000 genomes]
rs4851200	0.81[ASN][1000 genomes]
rs55867742	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59816625	0.82[ASN][1000 genomes]
rs60294863	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6708861	0.86[ASN][1000 genomes]
rs6709240	0.84[ASN][1000 genomes]
rs6711977	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6732397	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6734290	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6735381	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753588	0.83[ASN][1000 genomes]
rs71413827	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74177687	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7421284	0.81[ASN][1000 genomes]
rs7558074	0.83[ASN][1000 genomes]
rs7561616	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7570978	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571202	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7585721	0.83[ASN][1000 genomes]
rs7591212	0.83[ASN][1000 genomes]
rs7601470	0.83[ASN][1000 genomes]
rs7609108	0.86[ASN][1000 genomes]
rs901596	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
16	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
17	nsv961843	chr2:99916605-99924549	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13008948	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs13008948	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs13008948	REV1	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99879000-99933600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99892400-99935000	Weak transcription	Brain Angular Gyrus	brain
3	chr2:99894200-99934800	Weak transcription	Gastric	stomach
4	chr2:99895400-99935000	Weak transcription	Pancreas	Pancrea
5	chr2:99895800-99933600	Weak transcription	HSMM	muscle
6	chr2:99895800-99933600	Weak transcription	HSMMtube	muscle
7	chr2:99896800-99933400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:99897000-99933600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:99897200-99933800	Weak transcription	Fetal Intestine Small	intestine
10	chr2:99897400-99933800	Weak transcription	HepG2	liver
11	chr2:99898200-99934000	Weak transcription	Small Intestine	intestine
12	chr2:99898400-99938600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:99898600-99933800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:99899400-99933800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:99899600-99933000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:99899800-99935000	Weak transcription	Esophagus	oesophagus
17	chr2:99900000-99933600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:99900400-99933800	Weak transcription	Colonic Mucosa	Colon
19	chr2:99901200-99933400	Weak transcription	Primary B cells from cord blood	blood
20	chr2:99901200-99936600	Weak transcription	Fetal Brain Male	brain
21	chr2:99901400-99922800	Weak transcription	Ovary	ovary
22	chr2:99901600-99933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:99901600-99933600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:99901600-99933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:99901600-99933800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:99901600-99933800	Weak transcription	Fetal Intestine Large	intestine
27	chr2:99901600-99941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:99907800-99933800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:99908000-99934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:99908400-99933600	Weak transcription	A549	lung
31	chr2:99912400-99933600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:99913400-99933600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:99914800-99933800	Weak transcription	Lung	lung
34	chr2:99915000-99933400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:99915000-99933600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:99915000-99933600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:99915000-99942800	Weak transcription	Aorta	Aorta
38	chr2:99915200-99933600	Weak transcription	Thymus	Thymus
39	chr2:99915600-99933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:99916000-99935000	Weak transcription	Hela-S3	cervix
41	chr2:99916800-99933400	Weak transcription	Fetal Thymus	thymus
42	chr2:99917200-99934200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:99918400-99921400	Strong transcription	Liver	Liver
45	chr2:99918600-99923000	Strong transcription	Primary T cells from cord blood	blood
46	chr2:99918800-99921600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:99919000-99933600	Weak transcription	Brain Germinal Matrix	brain
48	chr2:99919000-99933800	Weak transcription	Spleen	Spleen
49	chr2:99919000-99935000	Weak transcription	Right Ventricle	heart
50	chr2:99919200-99933400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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