Variant report

Variant	rs2889611
Chromosome Location	chr10:49651748-49651749
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49631796..49633726-chr10:49649083..49652359,3	K562	blood:
2	chr10:49570787..49573176-chr10:49651060..49654395,3	MCF-7	breast:
3	chr10:49649966..49652141-chr10:49661563..49663221,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK8-1	chr10:49651168-49652001	XLOC_008482

Variant related genes	Relation type
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10508901	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1051507	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1051508	0.85[ASN][1000 genomes]
rs1051509	0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10745266	0.81[CHB][hapmap]
rs10776596	0.82[CHD][hapmap]
rs10776600	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10857560	0.82[CHD][hapmap]
rs10857561	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10857566	0.89[ASN][1000 genomes]
rs10857567	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101320	0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs11599396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345103	0.81[CHB][hapmap]
rs1919713	0.90[ASW][hapmap];0.88[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap]
rs2017750	0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2289805	0.80[CHD][hapmap]
rs2377351	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2440861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2463959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2463960	0.80[CHB][hapmap]
rs2698761	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2698767	0.91[EUR][1000 genomes]
rs2921271	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3789320	0.84[ASN][1000 genomes]
rs4838591	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838595	0.82[JPT][hapmap]
rs56078229	0.81[ASN][1000 genomes]
rs6537561	0.82[CHD][hapmap]
rs7075976	0.82[CHD][hapmap]
rs7086275	0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs7101060	0.82[CHD][hapmap]
rs72794398	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7912697	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8428	0.81[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs874208	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9888128	0.81[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1039508	chr10:49595718-49654403	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2889611	MAPK8	Cis_1M	lymphoblastoid	RTeQTL
rs2889611	MSMB	cis	parietal	SCAN
rs2889611	MAPK8	cis	normal skin	skin_eQTL
rs2889611	MAPK8	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49607600-49652400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:49612000-49664200	Weak transcription	Thymus	Thymus
3	chr10:49612800-49660200	Weak transcription	Aorta	Aorta
4	chr10:49619000-49664200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:49620800-49652400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:49620800-49658600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:49621200-49657400	Weak transcription	Brain Hippocampus Middle	brain
8	chr10:49621400-49652200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:49621400-49658600	Weak transcription	Brain Substantia Nigra	brain
10	chr10:49621400-49664400	Weak transcription	Brain Angular Gyrus	brain
11	chr10:49621600-49652200	Weak transcription	Fetal Heart	heart
12	chr10:49624600-49664800	Weak transcription	Gastric	stomach
13	chr10:49625800-49654400	Weak transcription	A549	lung
14	chr10:49626600-49664400	Weak transcription	Spleen	Spleen
15	chr10:49630400-49652400	Weak transcription	Pancreas	Pancrea
16	chr10:49635200-49652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr10:49635400-49652800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr10:49639000-49653000	Weak transcription	Fetal Stomach	stomach
19	chr10:49639400-49652600	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:49639600-49652400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr10:49639600-49657800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:49640000-49652200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr10:49640000-49652600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:49640400-49652200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:49641400-49652000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr10:49644000-49652600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr10:49644200-49651800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:49644200-49652800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:49644200-49653000	Weak transcription	Brain Germinal Matrix	brain
30	chr10:49644200-49655000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr10:49644200-49664400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:49644600-49656600	Weak transcription	HUVEC	blood vessel
33	chr10:49644600-49660400	Weak transcription	Brain Anterior Caudate	brain
34	chr10:49644800-49654800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:49646000-49653000	Weak transcription	Esophagus	oesophagus
36	chr10:49646000-49653200	Weak transcription	Fetal Brain Female	brain
37	chr10:49646200-49652600	Weak transcription	Right Ventricle	heart
38	chr10:49646200-49657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr10:49646400-49651800	Weak transcription	Fetal Brain Male	brain
40	chr10:49646400-49652200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:49646400-49652600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr10:49646400-49653000	Weak transcription	Left Ventricle	heart
43	chr10:49646400-49653200	Weak transcription	Placenta	Placenta
44	chr10:49646600-49653800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr10:49646600-49655200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr10:49647200-49651800	Weak transcription	Primary T cells from cord blood	blood
47	chr10:49647400-49653200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:49647800-49653200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr10:49647800-49663000	Weak transcription	NHEK	skin
50	chr10:49647800-49664400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links