Variant report

Variant	rs6879130
Chromosome Location	chr5:43013142-43013143
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10064003	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10941604	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10941605	0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11747435	0.91[ASN][1000 genomes]
rs11747714	0.95[JPT][hapmap]
rs11748821	0.83[EUR][1000 genomes]
rs11958008	0.91[ASN][1000 genomes]
rs12697439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13169690	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13170208	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13171133	0.88[ASN][1000 genomes]
rs13178479	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179934	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542369	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1574407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs160709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1618891	0.90[JPT][hapmap]
rs1624415	0.90[JPT][hapmap]
rs178415	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs186324	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes]
rs1902101	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100473	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124069	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs222060	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247280	0.90[AMR][1000 genomes]
rs2253450	0.91[ASN][1000 genomes]
rs2329994	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2329995	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548334	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes]
rs2548345	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2548349	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2548350	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2548353	0.88[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548356	0.88[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548373	0.91[AMR][1000 genomes]
rs2603620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2603634	0.91[AMR][1000 genomes]
rs2603644	0.95[JPT][hapmap]
rs2603656	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2882295	0.91[JPT][hapmap]
rs2924817	0.88[AMR][1000 genomes]
rs309909	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs309914	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs309921	0.86[AMR][1000 genomes]
rs309923	0.95[JPT][hapmap]
rs309924	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs309925	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs309926	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs309927	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs309948	0.91[AMR][1000 genomes]
rs309950	0.95[JPT][hapmap]
rs309951	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs316395	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316396	0.88[ASN][1000 genomes]
rs316400	0.85[ASN][1000 genomes]
rs316404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs316408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs316413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs316414	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316416	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs316419	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316422	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3909456	0.95[JPT][hapmap]
rs4033115	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4092293	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4092294	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296812	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs512921	0.91[JPT][hapmap]
rs515970	0.85[ASN][1000 genomes]
rs543569	0.85[ASN][1000 genomes]
rs557076	0.90[JPT][hapmap]
rs565761	0.85[ASN][1000 genomes]
rs567884	0.90[JPT][hapmap]
rs613825	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs643307	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451660	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451661	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6875214	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6892422	0.90[JPT][hapmap]
rs724430	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs768441	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7715065	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs782971	0.90[JPT][hapmap]
rs782978	0.90[JPT][hapmap]
rs782984	0.90[JPT][hapmap]
rs903391	0.91[JPT][hapmap]
rs9292862	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
11	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
12	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
13	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
14	esv2111843	chr5:43013142-43013143	Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43009000-43016200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:43009000-43016400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:43009000-43016600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:43009000-43017600	Weak transcription	Pancreas	Pancrea
5	chr5:43009400-43016600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:43009600-43013800	Weak transcription	HMEC	breast
7	chr5:43010000-43017400	Weak transcription	Esophagus	oesophagus
8	chr5:43010400-43017000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:43010400-43017400	Weak transcription	NHLF	lung
10	chr5:43010600-43016200	Weak transcription	Osteobl	bone
11	chr5:43010600-43017200	Weak transcription	HSMM	muscle
12	chr5:43010800-43016200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:43011000-43015200	Weak transcription	A549	lung
14	chr5:43011000-43016200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:43011000-43016400	Weak transcription	Placenta	Placenta
16	chr5:43011000-43016400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:43011000-43017600	Weak transcription	Gastric	stomach
18	chr5:43011000-43017600	Weak transcription	Lung	lung
19	chr5:43011200-43015600	Weak transcription	HUVEC	blood vessel
20	chr5:43011200-43016600	Weak transcription	NH-A	brain
21	chr5:43011200-43016800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:43011400-43014200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:43011400-43014400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:43011400-43015400	Weak transcription	Thymus	Thymus
25	chr5:43011400-43015600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:43011400-43016200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:43011400-43016400	Weak transcription	Spleen	Spleen
28	chr5:43011400-43017200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:43011400-43018200	Weak transcription	K562	blood
30	chr5:43011600-43014200	Weak transcription	Primary T cells from cord blood	blood
31	chr5:43011600-43014400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:43011600-43014400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:43011600-43015000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr5:43011600-43015000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:43011600-43015200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:43011600-43015400	Weak transcription	Fetal Thymus	thymus
37	chr5:43011600-43015600	Weak transcription	Hela-S3	cervix
38	chr5:43011600-43016400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:43011600-43016400	Weak transcription	NHDF-Ad	bronchial
40	chr5:43011800-43014400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:43011800-43015200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr5:43011800-43015200	Weak transcription	HepG2	liver
43	chr5:43011800-43015400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:43011800-43015400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:43011800-43015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:43011800-43016400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr5:43011800-43016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:43011800-43016600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:43012000-43015000	Weak transcription	GM12878-XiMat	blood
50	chr5:43012000-43015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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