Variant report

Variant	rs12662511
Chromosome Location	chr6:56417192-56417193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56406262..56407921-chr6:56416925..56419390,3	K562	blood:
2	chr6:56406220..56410337-chr6:56413126..56418049,5	MCF-7	breast:
3	chr6:56408981..56412253-chr6:56415239..56417908,3	K562	blood:
4	chr6:56416932..56418493-chr6:56421401..56422998,2	MCF-7	breast:
5	chr6:56413498..56416394-chr6:56417084..56419483,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16887983	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs17757606	0.87[ASN][1000 genomes]
rs17757660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17830661	0.87[ASN][1000 genomes]
rs17830685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17830715	0.90[ASN][1000 genomes]
rs17830726	0.90[ASN][1000 genomes]
rs17830810	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2281725	0.89[CHB][hapmap]
rs3800026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4256439	0.90[ASN][1000 genomes]
rs4288197	0.89[ASN][1000 genomes]
rs7769014	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56417200	Weak transcription	Fetal Brain Male	brain
2	chr6:56408200-56417400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:56408200-56419400	Weak transcription	Placenta	Placenta
4	chr6:56408200-56419800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56408400-56417400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:56408400-56417400	Weak transcription	HMEC	breast
10	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:56408600-56417200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:56408600-56417400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:56411400-56417400	Enhancers	Brain Substantia Nigra	brain
14	chr6:56411800-56419600	Weak transcription	A549	lung
15	chr6:56412000-56417600	Enhancers	Brain Anterior Caudate	brain
16	chr6:56412800-56418000	Enhancers	Rectal Smooth Muscle	rectum
17	chr6:56413200-56419600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:56413600-56417600	Enhancers	Brain Hippocampus Middle	brain
19	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:56414000-56419600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:56414200-56417400	Weak transcription	HUVEC	blood vessel
22	chr6:56414400-56418000	Genic enhancers	HSMM	muscle
23	chr6:56415200-56418400	Genic enhancers	HSMMtube	muscle
24	chr6:56415400-56417600	Genic enhancers	Muscle Satellite Cultured Cells	--
25	chr6:56415400-56427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:56415600-56417200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:56415600-56417400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:56415600-56417800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:56415600-56417800	Genic enhancers	Fetal Intestine Large	intestine
30	chr6:56415600-56418400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:56415800-56418200	Genic enhancers	NHDF-Ad	bronchial
32	chr6:56415800-56418400	Genic enhancers	Osteobl	bone
33	chr6:56415800-56418800	Enhancers	Colon Smooth Muscle	Colon
34	chr6:56415800-56419800	Weak transcription	NHEK	skin
35	chr6:56415800-56426000	Weak transcription	Ovary	ovary
36	chr6:56415800-56435200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:56416000-56417400	Enhancers	HepG2	liver
38	chr6:56416000-56419600	Weak transcription	Fetal Heart	heart
39	chr6:56416000-56420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:56416000-56421000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:56416200-56417200	Enhancers	Small Intestine	intestine
42	chr6:56416200-56417400	Enhancers	Right Ventricle	heart
43	chr6:56416200-56418600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:56416200-56418600	Strong transcription	Fetal Lung	lung
45	chr6:56416200-56418800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:56416200-56418800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:56416200-56419800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:56416200-56420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:56416200-56423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:56416400-56417400	Enhancers	Fetal Intestine Small	intestine

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