Variant report

Variant	rs2686838
Chromosome Location	chr7:48006649-48006650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48005406..48008358-chr7:48018655..48020435,2	MCF-7	breast:
2	chr7:47988986..47991046-chr7:48004400..48006975,2	MCF-7	breast:
3	chr7:48005343..48009057-chr7:48009774..48012451,3	K562	blood:

Variant related genes	Relation type
ENSG00000136273	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1056663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12702401	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13309127	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1879833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1879834	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242477	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242478	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242479	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686816	0.85[CHB][hapmap]
rs2686817	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs2686820	0.85[EUR][1000 genomes]
rs2686821	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686823	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2686825	0.85[EUR][1000 genomes]
rs2686830	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];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686831	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];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686833	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686834	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686835	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686839	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686840	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2686841	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686842	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708853	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708858	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708859	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708861	1.00[ASW][hapmap];0.96[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];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708865	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2708873	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708875	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708878	0.85[EUR][1000 genomes]
rs2708880	0.85[EUR][1000 genomes]
rs2708881	0.85[EUR][1000 genomes]
rs2708882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708894	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];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708896	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2708897	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708898	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708901	0.81[CEU][hapmap]
rs2708902	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708905	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708910	0.85[EUR][1000 genomes]
rs2708911	0.93[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs2952720	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3176478	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3176564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34016848	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35151200	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35536957	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4720624	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs57995674	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60107343	0.85[EUR][1000 genomes]
rs6944437	0.81[CEU][hapmap]
rs885337	0.92[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs939904	0.93[CEU][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs939905	0.93[CEU][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs953572	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953594	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9648569	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2686838	POLM	cis	parietal	SCAN
rs2686838	UPP1	cis	cerebellum	SCAN
rs2686838	HUS1	cis	cerebellum	SCAN
rs2686838	PKD1L1	cis	cerebellum	SCAN
rs2686838	ABCA13	cis	parietal	SCAN
rs2686838	UPP1	cis	multi-tissue	Pritchard
rs2686838	PKD1L1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999400-48008800	Strong transcription	H1 Cell Line	embryonic stem cell
2	chr7:47999600-48017600	Strong transcription	Primary T cells from cord blood	blood
3	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
4	chr7:48000200-48008400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:48000200-48008600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:48000200-48008600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:48000200-48008800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:48000200-48008800	Strong transcription	HSMM	muscle
9	chr7:48000200-48009400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:48000200-48009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:48000200-48016600	Strong transcription	Liver	Liver
12	chr7:48000200-48017800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:48000400-48007200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:48000400-48007400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:48000400-48007800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:48000400-48007800	Strong transcription	Fetal Brain Female	brain
17	chr7:48000400-48008200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr7:48000400-48008400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:48000400-48008400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr7:48000400-48008400	Strong transcription	Adipose Nuclei	Adipose
21	chr7:48000400-48008400	Strong transcription	Fetal Lung	lung
22	chr7:48000400-48008600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:48000400-48008600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:48000400-48008600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr7:48000400-48008600	Strong transcription	Stomach Smooth Muscle	stomach
26	chr7:48000400-48008600	Strong transcription	NH-A	brain
27	chr7:48000400-48008800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:48000400-48008800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:48000400-48009000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr7:48000400-48009000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:48000400-48009000	Strong transcription	Fetal Intestine Large	intestine
32	chr7:48000400-48009400	Strong transcription	Osteobl	bone
33	chr7:48000400-48009600	Strong transcription	A549	lung
34	chr7:48000400-48010000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:48000400-48011200	Strong transcription	Colon Smooth Muscle	Colon
36	chr7:48000400-48016800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:48000400-48017600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:48000400-48017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr7:48000400-48017600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:48000400-48017800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr7:48000400-48017800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:48000600-48007600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr7:48000600-48007800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr7:48000600-48007800	Strong transcription	Ovary	ovary
45	chr7:48000600-48008200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:48000600-48008400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr7:48000600-48008400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:48000600-48008400	Strong transcription	Brain Angular Gyrus	brain
49	chr7:48000600-48008400	Strong transcription	Brain Anterior Caudate	brain
50	chr7:48000600-48008600	Strong transcription	Primary B cells from cord blood	blood

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