Variant report

Variant	rs13202606
Chromosome Location	chr6:86340237-86340238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5E-1	chr6:86340107-86340251	ENSG00000236016.1
2	lnc-NT5E-1	chr6:86340080-86340995	ENSG00000236016.3

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13194512	0.91[EUR][1000 genomes]
rs13198956	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs13208740	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs16876340	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16876385	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1793	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs34239697	1.00[EUR][1000 genomes]
rs34898046	0.91[EUR][1000 genomes]
rs34936540	0.91[EUR][1000 genomes]
rs35121980	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35367106	1.00[EUR][1000 genomes]
rs35694036	0.91[EUR][1000 genomes]
rs35712823	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35988746	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36088473	0.91[EUR][1000 genomes]
rs3734442	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs3900740	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4707206	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4707213	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs55648312	0.91[EUR][1000 genomes]
rs55810446	0.91[EUR][1000 genomes]
rs67493405	0.91[EUR][1000 genomes]
rs6906121	0.91[EUR][1000 genomes]
rs6909402	0.91[EUR][1000 genomes]
rs6909654	0.91[EUR][1000 genomes]
rs6915519	0.87[EUR][1000 genomes]
rs71570763	0.84[EUR][1000 genomes]
rs71570764	0.91[EUR][1000 genomes]
rs71570766	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738371	0.91[EUR][1000 genomes]
rs7740830	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7742792	0.81[EUR][1000 genomes]
rs7771577	1.00[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:86314200-86341200	Strong transcription	HMEC	breast
3	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
6	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
10	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
15	chr6:86317000-86340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
22	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr6:86319400-86348600	Strong transcription	K562	blood
24	chr6:86319600-86342400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr6:86319600-86348200	Strong transcription	NHEK	skin
26	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:86320000-86348600	Strong transcription	Liver	Liver
30	chr6:86320200-86342400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:86320200-86350400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr6:86321000-86348600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:86321000-86349600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:86321200-86341200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:86323600-86349000	Strong transcription	Fetal Intestine Large	intestine
36	chr6:86323600-86351200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:86324800-86341400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:86324800-86348600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:86325400-86347000	Strong transcription	Hela-S3	cervix
40	chr6:86325600-86341200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:86326400-86349200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr6:86328000-86349800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:86330400-86342400	Weak transcription	Pancreas	Pancrea
44	chr6:86331400-86341200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:86331400-86348400	Strong transcription	NHDF-Ad	bronchial
46	chr6:86331400-86349000	Strong transcription	HSMM	muscle
47	chr6:86331600-86347400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:86331800-86347600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr6:86332200-86346600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:86332400-86349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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