Variant report

Variant	rs1196398
Chromosome Location	chr6:2254303-2254304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2244795..2247987-chr6:2252764..2255818,5	MCF-7	breast:
2	chr6:2250207..2252931-chr6:2253285..2256060,3	K562	blood:
3	chr6:2248443..2250050-chr6:2251800..2254441,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250903	Chromatin interaction
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1196386	1.00[AMR][1000 genomes]
rs1196391	1.00[AMR][1000 genomes]
rs1196392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1196395	1.00[AMR][1000 genomes]
rs1196397	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1486275	1.00[AMR][1000 genomes]
rs234921	1.00[AMR][1000 genomes]
rs234934	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2450308	1.00[AMR][1000 genomes]
rs335962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs335964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs634508	1.00[AMR][1000 genomes]
rs6925655	1.00[AMR][1000 genomes]
rs6931860	1.00[AMR][1000 genomes]
rs965754	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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	26 gene(s)	inside rSNPs	n/a
17	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
18	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
19	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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2246800-2254800	Weak transcription	Esophagus	oesophagus
2	chr6:2246800-2255800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:2246800-2264200	Weak transcription	Gastric	stomach
4	chr6:2247000-2254600	Weak transcription	Brain Substantia Nigra	brain
5	chr6:2247000-2254600	Weak transcription	Spleen	Spleen
6	chr6:2247000-2254600	Weak transcription	HSMM	muscle
7	chr6:2247000-2254800	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:2247000-2254800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:2247000-2255200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:2247000-2255400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:2247000-2258600	Weak transcription	Colonic Mucosa	Colon
12	chr6:2247000-2260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:2247000-2264200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:2247000-2264400	Weak transcription	HSMMtube	muscle
15	chr6:2247000-2264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:2247000-2265200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:2247000-2265200	Weak transcription	Osteobl	bone
18	chr6:2247000-2269400	Weak transcription	Right Ventricle	heart
19	chr6:2247000-2273800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:2247000-2275000	Weak transcription	Fetal Kidney	kidney
21	chr6:2247000-2275400	Weak transcription	NHLF	lung
22	chr6:2247000-2275600	Weak transcription	Fetal Heart	heart
23	chr6:2247200-2254800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:2247200-2254800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:2247200-2254800	Weak transcription	Fetal Lung	lung
26	chr6:2247200-2256800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:2247200-2264400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:2247200-2272600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:2247600-2274400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:2247800-2284200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:2248000-2254400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:2248200-2275000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:2248400-2264200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:2248400-2274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr6:2248600-2257600	Weak transcription	Stomach Mucosa	stomach
36	chr6:2248600-2258200	Weak transcription	Small Intestine	intestine
37	chr6:2248600-2264400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:2249000-2255800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr6:2249000-2256400	Strong transcription	Liver	Liver
40	chr6:2249200-2256600	Strong transcription	Fetal Intestine Large	intestine
41	chr6:2249200-2256600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:2250000-2254600	Weak transcription	Placenta	Placenta
43	chr6:2250400-2254800	Weak transcription	Adipose Nuclei	Adipose
44	chr6:2250400-2255000	Weak transcription	Brain Anterior Caudate	brain
45	chr6:2250400-2264200	Weak transcription	Pancreas	Pancrea
46	chr6:2250400-2267600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:2250400-2274800	Weak transcription	Brain Angular Gyrus	brain
48	chr6:2250600-2254800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:2250800-2265400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:2251000-2254400	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links