Variant report

Variant	rs2181905
Chromosome Location	chr13:49878236-49878237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49870136..49872971-chr13:49876994..49878672,2	MCF-7	breast:
2	chr13:49877297..49879495-chr13:49894000..49896980,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10459375	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10459376	0.93[EUR][1000 genomes]
rs11619804	0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs11838927	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11843587	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12585196	0.96[CEU][hapmap];0.97[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1555672	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924659	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1924660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs1924661	0.87[EUR][1000 genomes]
rs2038759	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2147398	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274149	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2274150	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2407521	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2407607	0.88[EUR][1000 genomes]
rs2407608	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2407609	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs3087770	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3751418	0.83[JPT][hapmap]
rs3764131	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs4245351	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4941637	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942809	0.86[EUR][1000 genomes]
rs4942811	0.87[EUR][1000 genomes]
rs4942812	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942815	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6561511	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs719614	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs7320595	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7320745	0.87[EUR][1000 genomes]
rs7326181	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7326191	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs7328063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7330892	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7334929	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7984689	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs7988621	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7997545	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7999710	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9316434	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs9316437	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9316439	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs9526532	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs9526533	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs9526534	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs9526537	0.87[EUR][1000 genomes]
rs9526538	0.88[EUR][1000 genomes]
rs9526539	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535173	0.85[EUR][1000 genomes]
rs9535174	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9535177	0.87[EUR][1000 genomes]
rs9535180	0.80[CHB][hapmap];0.87[EUR][1000 genomes]
rs9535181	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs9535182	0.87[EUR][1000 genomes]
rs9535184	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs9535185	0.88[EUR][1000 genomes]
rs9535190	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535192	0.85[EUR][1000 genomes]
rs9535193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535194	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535197	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535198	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535199	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535200	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9562873	0.86[EUR][1000 genomes]
rs9568176	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568177	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568179	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568181	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9568182	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9591249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9596077	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9596078	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596079	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596080	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9596082	0.90[ASN][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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2181905	LCP1	cis	parietal	SCAN
rs2181905	CTSLL3	cis	Liver	GTEx
rs2181905	CAB39L	cis	multi-tissue	Pritchard
rs2181905	CAB39L	cis	cerebellum	SCAN
rs2181905	CAB39L	cis	Liver	GTEx
rs2181905	CTSLL3	trans	multi-tissue	Pritchard

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49854000-49883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49867200-49884200	Weak transcription	Fetal Brain Female	brain
3	chr13:49869200-49879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr13:49869600-49882200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:49871600-49880400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr13:49872200-49878600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:49875200-49880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:49875400-49878600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr13:49875800-49878400	Enhancers	Brain Hippocampus Middle	brain
10	chr13:49875800-49878400	Enhancers	Brain Substantia Nigra	brain
11	chr13:49875800-49878400	Enhancers	Fetal Muscle Trunk	muscle
12	chr13:49875800-49879000	Weak transcription	Fetal Kidney	kidney
13	chr13:49875800-49879400	Enhancers	Brain Angular Gyrus	brain
14	chr13:49875800-49881400	Weak transcription	Fetal Lung	lung
15	chr13:49875800-49883800	Weak transcription	Fetal Intestine Small	intestine
16	chr13:49875800-49884000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr13:49875800-49884200	Weak transcription	Primary T cells from cord blood	blood
18	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
19	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr13:49876000-49879800	Weak transcription	Primary B cells from cord blood	blood
22	chr13:49876000-49880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:49876000-49881400	Weak transcription	Stomach Mucosa	stomach
24	chr13:49876000-49881600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:49876000-49882200	Weak transcription	Placenta	Placenta
26	chr13:49876000-49884000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr13:49876200-49879000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr13:49876200-49879800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:49876200-49884200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr13:49876200-49884200	Weak transcription	Brain Germinal Matrix	brain
31	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:49876400-49878400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:49876400-49887800	Weak transcription	Colonic Mucosa	Colon
35	chr13:49876400-49887800	Weak transcription	Fetal Heart	heart
36	chr13:49876400-49887800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr13:49876600-49879000	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:49876600-49879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr13:49876800-49878600	Enhancers	HMEC	breast
40	chr13:49877000-49878400	Enhancers	Duodenum Mucosa	Duodenum
41	chr13:49877000-49878800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr13:49877000-49879000	Enhancers	Spleen	Spleen
43	chr13:49877000-49879400	Enhancers	Pancreas	Pancrea
44	chr13:49877200-49879000	Enhancers	Lung	lung
45	chr13:49877200-49883800	Enhancers	Adipose Nuclei	Adipose
46	chr13:49877400-49878400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr13:49877400-49878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr13:49877400-49878600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr13:49877400-49878600	Enhancers	Right Atrium	heart
50	chr13:49877600-49878400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links