Variant report

Variant	rs2860998
Chromosome Location	chr10:96998519-96998520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1049814	0.82[CHB][hapmap];0.83[LWK][hapmap];0.89[YRI][hapmap]
rs1049961	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11188220	0.89[JPT][hapmap]
rs11188243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11188244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12771349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778613	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12778837	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026680	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2860999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61868350	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs61868351	0.96[ASN][1000 genomes]
rs7909905	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910217	0.82[AFR][1000 genomes]

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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2860998	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96990800-97005200	Weak transcription	Psoas Muscle	Psoas
2	chr10:96991000-96999800	Weak transcription	Fetal Lung	lung
3	chr10:96991000-97001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:96991000-97001600	Weak transcription	Thymus	Thymus
5	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:96991000-97006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:96991000-97006600	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:96991000-97006600	Weak transcription	Right Atrium	heart
10	chr10:96991000-97007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr10:96991000-97020400	Weak transcription	Fetal Muscle Leg	muscle
12	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr10:96991200-97000000	Weak transcription	Fetal Kidney	kidney
14	chr10:96991200-97000200	Weak transcription	Fetal Thymus	thymus
15	chr10:96991400-97019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:96991600-97001000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:96992000-97005000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr10:96992000-97005800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:96992200-97009000	Strong transcription	Liver	Liver
20	chr10:96992400-96998600	Strong transcription	Fetal Stomach	stomach
21	chr10:96992400-96998800	Strong transcription	Left Ventricle	heart
22	chr10:96992400-96999000	Strong transcription	Adipose Nuclei	Adipose
23	chr10:96992400-97000000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:96992400-97006200	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr10:96992600-96998600	Strong transcription	Lung	lung
26	chr10:96992600-97004000	Strong transcription	Fetal Intestine Large	intestine
27	chr10:96993200-96998800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:96994600-96998600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:96994600-96998600	Strong transcription	Colonic Mucosa	Colon
30	chr10:96994800-96998600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:96994800-96998600	Strong transcription	Gastric	stomach
32	chr10:96994800-96998600	Genic enhancers	HMEC	breast
33	chr10:96995200-97002600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:96995400-96998600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:96995400-97000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:96995600-96998600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:96995800-96998600	Strong transcription	HepG2	liver
38	chr10:96996200-96998600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr10:96996200-96998600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:96996200-97001800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr10:96996200-97004000	Strong transcription	Fetal Intestine Small	intestine
42	chr10:96996200-97006600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr10:96996400-96998600	Strong transcription	Right Ventricle	heart
44	chr10:96996400-96999800	Weak transcription	Primary B cells from cord blood	blood
45	chr10:96996400-97016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr10:96996600-96998600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr10:96996600-96999000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr10:96996600-97000000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr10:96996600-97007000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr10:96996800-96998600	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links