Variant report

Variant	rs1196390
Chromosome Location	chr6:2261765-2261766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1196389	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196394	0.92[ASN][1000 genomes]
rs1196396	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475411	0.90[AMR][1000 genomes]
rs1486274	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1629950	0.92[ASN][1000 genomes]
rs1684153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887418	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1887420	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148824	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs234920	0.85[ASN][1000 genomes]
rs2450301	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2450303	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2450306	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2450311	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2478999	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2479000	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2479003	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2479005	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2479009	0.88[AMR][1000 genomes]
rs2479010	0.90[AMR][1000 genomes]
rs2479012	0.89[AMR][1000 genomes]
rs2479015	0.93[ASN][1000 genomes]
rs2479016	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2505656	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2505665	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2505668	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2505669	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2505672	0.89[AMR][1000 genomes]
rs2505674	0.89[AMR][1000 genomes]
rs335963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959648	0.89[AMR][1000 genomes]
rs62392643	0.89[AMR][1000 genomes]
rs6596876	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6939099	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7765735	0.89[AMR][1000 genomes]
rs7766115	0.89[AMR][1000 genomes]
rs9328086	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392379	0.89[AMR][1000 genomes]
rs9392382	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9405552	0.84[AMR][1000 genomes]
rs9501828	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
9	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
17	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
18	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2246800-2264200	Weak transcription	Gastric	stomach
2	chr6:2247000-2264200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:2247000-2264400	Weak transcription	HSMMtube	muscle
4	chr6:2247000-2264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:2247000-2265200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:2247000-2265200	Weak transcription	Osteobl	bone
7	chr6:2247000-2269400	Weak transcription	Right Ventricle	heart
8	chr6:2247000-2273800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:2247000-2275000	Weak transcription	Fetal Kidney	kidney
10	chr6:2247000-2275400	Weak transcription	NHLF	lung
11	chr6:2247000-2275600	Weak transcription	Fetal Heart	heart
12	chr6:2247200-2264400	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:2247200-2272600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:2247600-2274400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:2247800-2284200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:2248200-2275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:2248400-2264200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:2248400-2274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:2248600-2264400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:2250400-2264200	Weak transcription	Pancreas	Pancrea
21	chr6:2250400-2267600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:2250400-2274800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:2250800-2265400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:2251000-2264200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:2251000-2273600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:2251200-2264200	Weak transcription	Thymus	Thymus
27	chr6:2252200-2264800	Weak transcription	Fetal Thymus	thymus
28	chr6:2252400-2265800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:2255000-2264200	Weak transcription	HSMM	muscle
30	chr6:2255200-2264200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:2255200-2264200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:2255200-2264200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:2255200-2264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:2255200-2264200	Weak transcription	Spleen	Spleen
35	chr6:2255200-2272400	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:2255400-2264200	Weak transcription	Brain Anterior Caudate	brain
37	chr6:2255400-2264200	Weak transcription	Esophagus	oesophagus
38	chr6:2255400-2264200	Weak transcription	Ovary	ovary
39	chr6:2255400-2264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:2255400-2265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:2255400-2272800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:2255600-2264200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:2255600-2264400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:2255600-2269600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:2255800-2264200	Weak transcription	Dnd41	blood
46	chr6:2255800-2264200	Weak transcription	GM12878-XiMat	blood
47	chr6:2255800-2264400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:2255800-2288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:2256000-2263800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:2256000-2264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links