Variant report

Variant	rs2239541
Chromosome Location	chr6:36494053-36494054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36492697..36495069-chr6:36562031..36564284,2	K562	blood:
2	chr6:36487455..36494660-chr6:36559051..36563997,8	MCF-7	breast:
3	chr6:36492328..36495543-chr6:36512590..36515931,4	K562	blood:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000112079	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12525802	0.83[ASN][1000 genomes]
rs16888605	0.80[ASN][1000 genomes]
rs16888788	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1885206	0.81[AMR][1000 genomes]
rs2267930	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273882	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273883	0.86[AMR][1000 genomes]
rs3778028	0.82[AMR][1000 genomes]
rs3819759	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41272166	0.83[ASN][1000 genomes]
rs4236051	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711451	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713976	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713977	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713978	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv5260	chr6:36471464-36516119	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36456400-36512600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:36463000-36507200	Weak transcription	Fetal Brain Male	brain
3	chr6:36463800-36513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:36470600-36498800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:36473600-36500000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:36474000-36495200	Weak transcription	Fetal Heart	heart
7	chr6:36476200-36497800	Strong transcription	Dnd41	blood
8	chr6:36476800-36512200	Weak transcription	Brain Angular Gyrus	brain
9	chr6:36477400-36507400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr6:36478400-36507400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:36478400-36507800	Strong transcription	Fetal Thymus	thymus
12	chr6:36478400-36513600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:36478400-36514000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:36478800-36497400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:36478800-36512400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:36479600-36514400	Weak transcription	Spleen	Spleen
17	chr6:36480200-36496000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:36481400-36512000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:36482200-36494200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:36483200-36500000	Weak transcription	Lung	lung
21	chr6:36484200-36506200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:36484600-36507600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:36484600-36514000	Weak transcription	Pancreas	Pancrea
24	chr6:36484800-36512400	Weak transcription	Right Atrium	heart
25	chr6:36485800-36494200	Strong transcription	Fetal Intestine Large	intestine
26	chr6:36487000-36494200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:36487000-36494200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr6:36487400-36505400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:36488000-36496000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:36488800-36513800	Weak transcription	Aorta	Aorta
31	chr6:36489400-36496600	Weak transcription	Hela-S3	cervix
32	chr6:36490000-36494600	Strong transcription	Fetal Stomach	stomach
33	chr6:36490200-36507000	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:36491200-36494200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr6:36491400-36494600	Strong transcription	Thymus	Thymus
36	chr6:36491600-36503000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:36491800-36512400	Weak transcription	Small Intestine	intestine
38	chr6:36492000-36507600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:36492200-36495200	Weak transcription	Psoas Muscle	Psoas
40	chr6:36492200-36496000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:36492200-36499200	Weak transcription	A549	lung
42	chr6:36492400-36495200	Weak transcription	Fetal Lung	lung
43	chr6:36492400-36501000	Weak transcription	Ovary	ovary
44	chr6:36492400-36507200	Weak transcription	Fetal Kidney	kidney
45	chr6:36492400-36514000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:36492600-36494200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:36492600-36494400	Enhancers	NHEK	skin
48	chr6:36492600-36495800	Strong transcription	Fetal Intestine Small	intestine
49	chr6:36492800-36494400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:36492800-36494400	Enhancers	Liver	Liver

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